Power Loss?

I have a 2001 Chevy Silverado Ext cab.  I am using a Pioneer DEH-P8500MP head unit.  The rest is pretty much listed.  Today I removed the remote bass control off of the Memphis ST1000D and installed the remote knob that goes on the patch cords.  This is what I used on my original amp.  Occasionally, when the bass hits, it causes my 61/2" door speakers to make a crack noise.  Not all of the time, but on occasion.  But when I turn the gain completely down on my subs, there is no crack whatsoever.  That is why I was thinking there is a power loss going to the amps.  Supposedly, with the 1000d and the 3004, I should be running around 1300 watts.  I have it on 1 punch 1.0 farad capacitor.  I am waiting for a second one which I should be getting at the end of the week.  This was I can run each amp on its own cap.  Does any one think this might solve the problem?  I just changed the gain control, so I don,'t know if that has fixed the problem.  Have not tried it yet.

My truck is a 2001 Chevy Silverado ext. cab.  The head unit is a Pioneer DEH-P8500MP.  I also noticed today that on occasion, when the subs hit, that the door speakers make a crack noise.  This is why I was wondering about the power loss.  I have both amps on a Punch 1.0 farad cap.  The subs are Memphis M Class DVC, and the door speakers are Ultra linear 6 1/2.  I plan to get another cap by the end of the week so that I can run a cap to each amp.  I also changed the gain control on the ST1000D, from the factory one that runs through the patch cables.  Any other suggestions?