Its hard to say how to fix this problem really. Are you stil using your factory amp? You should be because the crossovers are still contained in it and your deck is not capable of powering 10 speakers so I will assume you are.
Sometimes people wire in PAC OEM2 or equivalent premium sound adapters, which is simply not needed in our e34's.
You deck should be wired directly to the speaker leads (which are really the amps 4 inputs) using only the positive wires and all the negative leads should be connected together. YOur remote turn on wire (blue/white) should power the factory turn on wire (white)
THis is the way all e34's should be wired.
Perhaps you have wired one or more of your speakers backward results in a out of phase system. Double check your speaker polarity.
More details will get you a more detailed troubleshooting.
Greg Mannino
Car Audio.Video.Security.Navigation Guru
Electrical/Mechanical Specialist