well, before you go about fixing anything, you need to diagnose the problem. Try using the different stuff involved with new sets of stuff you know to be working. First, try swapping out the patch cables. Still bad? hook up the pre-outs to another amplifier or literally anything you can find laying around that takes RCA inputs. Still bad, try a different source with your current amp. Then you can decide what to do about it.
I have tried diffrent amps and there both do the same thing and when i put in the system it sounded great and then i got a new deck and it sounded good for a couple weeks then it started making loud thumping with the volume on zero and then i would rehook up my old deck and it wouldnt do i dunno why mabye because my new deck is more power full or somthin but now both decks are doin the same thing,i was thinking it was the rca jacks but i dunno?
did you readjust the amp gain after replacing the HU? You're troubles could be caused by having your gain set too high. The purpose of setting the gain is to match up the HU's voltage output with the amp's expected voltage input, which it then raises to a certain output voltage where it will perform correctly. Also, who's your HU made by? If its of marginal quality, that would explain a lot. Thats a strange senario though, now neither deck works with either amp...this is where I'd need to test everything out.
MY Hu is made by pioeer, and i lost my book on it so i dont where to see my level at. but i belive i found the problem i got a new groud wire and put the ground in a better spot it works but i dunno if that will do it i will half to see.