My E46 is a 'vert, but I'll assume that the E46 sunroofs are much the same as those in the E39. It could be several things. The motor turns a gear that moves this cable assembly back and forth along tracks. Attached to that track are plastic "shoes" that attach to the sunroof popup arms and control the lifting of the sunroof as well as its back-and-forth movement. This is a vast oversimplification. The most common failure is that these plastic bits disintegrate. When you go to pop up the sunroof and you hear a crack, and one side or the other doesn't go up, you know one has broken.
So, it's probably this, although it's possible that the gear mechanism that the motor fits into is botched up.
Regardless, you have to pull the sunroof cassette out in order to do repairs on it. It's a royal PITA. The entire headliner has to be removed, then the entire cassette unbolts. Good luck.
Current stable:
2002 525i (Daily Driver)
1994 SN95 Mustang 'Vert (The Bumblebee)
2001 325i Convertible (Beach cruiser project)
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