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Thread: 540i automatic 'Clunk' sound

  1. #1
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    540i automatic 'Clunk' sound

    Hi all,

    I recently bought a 2001 E39 540i automatic. It has no trouble with shifting during driving, but I noticed a 'clunk' sound when changing the gear lever from any position to D or R. It also makes a clunking sound when trying the accelerate from a stop. When I'm at a traffic light and I try to pull away, there is a distinctive sound coming from beneath the car.

    Also when driving around 100km/h (60mph) there is a whining noise coming from the back. It changes pitch as I gain speed, but is most noticable at 60mph. At the same time there is a slight vibration in the steering wheel.

    Now I don't know these two problems are related, but I myself suspect the drive shaft middle bearing. Do you have any other idea's what this might be?

    thanks in advance!

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    No problem. Yeah, the whole driveshaft system sshould be checked. There's a flex disk aka "Guibo" (which theoretically is pronounced "JewBo" but in the real world everybody says "GweeBo") that easily could be cracked and sloppy... and there's the center U-joint and bearing, and then there's the actual CV joint, . What you describe is almost certainly one or several or all of those things needing service.

    The other long shot possibility is a differential problem / rear axle problem but honestly that's far less likely than the driveshaft. Have that all checked out. Over here you can just swap for a rebuilt driveshaft that's like new, or, you can get the parts yourself. There's a few small tricks like being sure you get the center bearing back where it was and ensuring the guibo is installed in the right orientiation its not hard.
    Last edited by geargrinder; 01-10-2019 at 10:20 AM. Reason: List the DS parts in physical order to make better sense
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    2014 BMW X1 xDrive28i (wifemobile)

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  3. #3
    JimLev's Avatar
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    And while your under the car checking the driveshaft it would be a good time to change the diff fluid, it possibly has never been done before, same for the tranny unless your one of those that believes the old fluid is "holding the tranny together".

    Mark the outline of the center support bracket on the body so you can put it back in the same position it was in.

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    So how do you check the driveshaft visually? Other than looking at the guibo and trying to rotate it manually and check for any visual play, what else to look for?

    I have a vibration at about 80 mph on the DINAN 7 and its not suspension related since thats all new up front.

    02 e39 540i Sport (Son), 01 DINAN 7 (Me), 12 e70 X5 x35i (Mrs), 95 e34 525i (Daughter 2), 01 e46 325Ci vert (Daughter 1)

  5. #5
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    Thanks all for the quick answers. I live in a city center so working on the car on the street is not an option. Luckily I can rent a hobby workshop with a hydraulic lift, so I will soon make an appointment. When I'm at it, I will also change the gearbox and differential fluids.
    Are there any cheap tools I can perform a flush with? Like an electric pump or so?

  6. #6
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    No special tool needed for a simple drain and fill of the differential fluid, or the gearbox (transmission) fluid.

    -- Loosen the fill plug,
    -- unscrew the drain plug,
    -- Drain the fluid,
    -- Re-screw the drain plug,
    -- Un-screw the fill plug,
    -- Refill with fresh new appropriate fluid -using an air pump-,
    -- Screw the fill plug.

    You may want to replace the plugs and their gaskets when doing this procedure.

    Also, no need for hydraulic lift to change those fluids. You can crawl under the car to change the differential fluid- a pretty easy job really. And you can jack up the right side of the front of the car to drain and fill the transmissions fluid.
    Last edited by Chedley; 01-11-2019 at 05:00 AM.

  7. #7
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    Quote Originally Posted by kouks View Post
    So how do you check the driveshaft visually? Other than looking at the guibo and trying to rotate it manually and check for any visual play, what else to look for?

    I have a vibration at about 80 mph on the DINAN 7 and its not suspension related since thats all new up front.
    Visually for the guibo.
    For the center support bearing and the rear CV joint you can try to move it up/down, left/right using a lot of muscle on it, shouldn't move if it's good.

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    Fluid change tip: Remove the fill plug first, before draining the fluid out and finding that the fill plug is frozen shut!
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    Quote Originally Posted by Chedley View Post
    No special tool needed for a simple drain and fill of the differential fluid, or the gearbox (transmission) fluid.

    -- Loosen the fill plug,
    -- unscrew the drain plug,
    -- Drain the fluid,
    -- Re-screw the drain plug,
    -- Un-screw the fill plug,
    -- Refill with fresh new appropriate fluid -using an air pump-,
    -- Screw the fill plug.

    You may want to replace the plugs and their gaskets when doing this procedure.

    Also, no need for hydraulic lift to change those fluids. You can crawl under the car to change the differential fluid- a pretty easy job really. And you can jack up the right side of the front of the car to drain and fill the transmissions fluid.
    Drain and fill an auto trans is much more than this.

    1. Cool or cold trans, car on jacks and level
    2. Loosen fill plug
    3. Remove drain plug and let drain for about 15 minutes. This let’s as much fluid as possible out of the drums and valve body. There will be fluid in the torque converter that will not drain. More on that later.
    4. Replace drain plug
    5. Remove fill plug and fill with correct trans fluid until it overflows, leave it open
    6. Start engine, hold brake, cycle trans through teach gear for 10 seconds each, go back to P, keep engine running
    7. Fill trans with more fluid until it overflows again, trans temp should be less than about 80 deg
    8. Replace fill plug
    9. Turn off engine.

    To get the fluid that was left in the torque converter, you need to drive the car a few days to let the old and new oil mix, then lather, rinse, repeat the process. It will take a total of three times to have nearly new oil.

    Or you can take it to any trans shop and ask for a fluid flush and get it done in a couple hours.

    Its very important you use the OE fluid, you cannot mix different kinds of fluid.
    Last edited by kouks; 01-12-2019 at 12:21 AM.

    02 e39 540i Sport (Son), 01 DINAN 7 (Me), 12 e70 X5 x35i (Mrs), 95 e34 525i (Daughter 2), 01 e46 325Ci vert (Daughter 1)

  10. #10
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    Quote Originally Posted by kouks View Post
    Drain and fill an auto trans is much more than this.

    …..
    To get the fluid that was left in the torque converter, you need to drive the car a few days to let the old and new oil mix, then lather, rinse, repeat the process. It will take a total of three times to have nearly new oil.

    Or you can take it to any trans shop and ask for a fluid flush and get it done in a couple hours.

    Its very important you use the OE fluid, you cannot mix different kinds of fluid.
    I would strongly advise AGAINST fluid flush in the trans shops.
    Best to do 2 or 3 drain-and-refills spaced over a few days or weeks or even months, using the same new correct transmission fluid. (I use and recommend Pentosin-ATF-1 Synthetic)
    Last edited by Chedley; 01-12-2019 at 12:41 AM.

  11. #11
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    Good summary kouks. Actually on the ZF autos I think there's a min-temp too. So ideally you have a computer or scanner plugged in live monitoring temp. For sure if you don't do the routine and just try the "drain and fill" you'll likely be underfilled.
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  12. #12
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    update: another problem happened although I'm not sure if it's related. I was driving to work today and all of a sudden a got a notification: transmission failsafe.
    I hooked up my laptop to see if I could find any error codes on the trans but all I could find was '151 CAN Brake signal'. Or I'm checking in the wrong place for codes. The car shifted gears as usually, other then the notification nothing strange happened.
    Last edited by jigsaw88; 01-15-2019 at 12:54 PM.

  13. #13
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    Check your battery and alternator.
    Low battery charge or failing alternator are well known to cause the mysterious "Transmission Failsafe".

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    For draining the transmission, the minimum temperature is 40°C. Although there's not a single reference to the transmission needing to be "cold" as per ZF instructions. Most official ZF guys will tell you to drain at operating temperature and let it drain for as long as you want to (hour at the least, more is better) and after it has cooled down while draining, start the engine for about 30 seconds and stop it without touching the throttle or anything else than starting it in N and stop it after 30 seconds. Then yes, fill cold, check level at minimum temp of ~60°C

    - - - Updated - - -

    Quote Originally Posted by Chedley View Post
    Check your battery and alternator.
    Low battery charge or failing alternator are well known to cause the mysterious "Transmission Failsafe".
    this times a million. Many times a crapping out VR will send the data TX into "bonkus" mode causing all sort of odd behaviors amongst which are the tranny failsafe.
    Diehard E39 driver.
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    Quote Originally Posted by jicaino View Post

    - - - Updated - - -


    this times a million. Many times a crapping out VR will send the data TX into "bonkus" mode causing all sort of odd behaviors amongst which are the tranny failsafe.

    Mm, does this also explain why my car is unable to start beceause of a flat battery when I leave the ignition on for 10 minutes?
    I can leave my car outside for a week and it will start. I can't leave my radio or ignition on for 10 minutes cs then the battery is flat. Really weird.

  16. #16
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    Quote Originally Posted by jigsaw88 View Post
    Mm, does this also explain why my car is unable to start beceause of a flat battery when I leave the ignition on for 10 minutes?
    I can leave my car outside for a week and it will start. I can't leave my radio or ignition on for 10 minutes cs then the battery is flat. Really weird.
    Typical. These cars suck a ton of power with ignition in position 2 and engine off. Not good cars to leave keys or radio on in. I suspect using that feature w/ key off and turning radio on that that still 'un-sleeps' the whole car and thats why even just listening to radio takes a fair amount of juice.
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    10 minutes is an awful short time period for the battery to run down enough to where it wont start. id consider having the battery tested.

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    Quote Originally Posted by geargrinder View Post
    Typical. These cars suck a ton of power with ignition in position 2 and engine off. Not good cars to leave keys or radio on in. I suspect using that feature w/ key off and turning radio on that that still 'un-sleeps' the whole car and thats why even just listening to radio takes a fair amount of juice.
    Of course. And if you factor in the additional gizmos powered by the cigar lighter : rea-view backup camera, cell phone charger, wonder why the battery flattens in 15 minutes or so...

  19. #19
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    I hooked up my computer to search for error codes. I think it's not normal to drain a battery this fast in 15 minutes. How are you supposed to vacuum clean your car this way with doors open and interior lights on? I suspect a sulfurized battery. It holds just enough charge to start the car the next go, but not enough to provide long enough power. I first noticed it when I was able to park my car for two weeks, but not start the pre-heater, then it died in a few mins. I will hook up my battery reconditioner this weekend
    Last edited by jigsaw88; 01-17-2019 at 04:40 AM.

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    Yes that could be. You can leave the doors open, that's no issue because if you don't touch anything for about 15mins, the whole car goes "to sleep" as long as you don't open / close another door. I'm talking about extended ignition on / radio on situations. But yes indeed your battery could be bad for sure.
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    Last time I checked the draw on the battery with the key on, engine off, it was 20-25 amps. An old battery isn't going to last that long. When you open the doors and the car wakes up you can shut off all the interior lights if you push the center overhead button in the roof panel.

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    I'd replace the battery after I check for proper VR function. Those are notorious for starting to "spike up" here and there, frying electronic modules and battery and sending data TX into weird failsafes and such. Happens when you're driving at operating temp under relatively hot conditions (engine heat soked or such) and you suddenly rev it up good.

    It took forever for me to diagnose the crapping out VR because it was all good under static test conditions, battery held charge and all, and all of a sudden EGS started to act up, followed by DME and whatnot. I ended up with a toasty DME and a dead battery because I was certain my alternator was good because I had taken care of it in the previous months.
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