Had a full system installed and when using Aux cable into Audio Control LC8i, it sounds fantastic.

However, anything from stock head unit sounds bad, works, but does not sound good.

It is my understanding that stereo shop went:

H/K Stock Head Unit -> Stock Amp -> LC8i -> 2 JL Amps (1 to 10" JL10W6, 1 8Channel JL amp to all other speakers, minus Center Channel (which is still hooked to Factory Amp).
All speakers minus center channel, where changed to JL 4" C2s, and JL tweeters.

Again, iPhone via Aux cable to LCi, all good, so system itself is not the problem.

When using CD/Satellite/Terrestrial Audio via head unit, the quality of the audio leaves a lot to be desired.
1. there is a hiss from speakers, when volume is not set to zero (not related to engine RPMs, not there when using Aux cable into LC8)
2. Volume 0 to volume 1 (one click of volume knob) is above conversational audio level
3. I noticed today, that when fading, it sounds like audio is only coming from channels 1-2 (front door speakers). I was driving when i had this epiphany, need to verify.

I believe something is not wired correctly.

I am working with the stereo shop to try and fix, but wanted to get an independent opinion.

Thanks