Hi!
Driving an E46, but from my experience the sound systems (if Harman Kardon and Nav Pro) are pretty much the exact the same.
Yesterday when I stopped for gas and had the ignition off for a couple of minutes, something really weird happened. I'm running a H/K system, 16:9 Navi and bluetooth phone, factory installed BMW (and I'm actually happy with the original sound) and I have only added an aftermarket dvd-player and a tv-module and it works great.
Anyhow, I started my car and the most super-dissorting and clippy sound (the bass amplifies x100) come from the entire system. Something is very, very wrong here.
However, the bluetooth phone sound is fine and also the navigation system sound. Well, as fine as it can be on these systems (is the phone and navigation sound also amplified in the H/K amp or how does it work?) Other than that, the all other sound (CDC, Tape and Radio) is absolutely horrible and either something is broken, or well I have no clue...

The sound is so horribly bassy and "clippy" that I dont dare keeping the units on at all.
I tried disconnecting the battery (negative only, does it make any difference?), no luck... Also disconnected the TV-input module and no luck there either. I am a bit scared it could be the TV-input that for some reason has ruined my system, dont know...
Had the rear deck out this weekend (to suede it) and had the rear H/K's out, could there be a short in the rear speaker cables? Could a speker cable short do this to a complete system? Wierd how the phone and nav sound works fine, isnt it?
Could it be the radio module? Could it be the H/K Amp, do they often break down? Please help me, where do I start...?