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because improperly setting the input sensitivity of the amplifier overdrives the input stage of the amplifier, causing distortion. Essentially you're sending too much voltage to the input of the amplifier and causing teh signal waveform to clip. Turn the 'gain' up too high on any amp and it will either get noise, a whine, or go into thermal protection mode most times.

see the 'audio amplifier fundamentals' FAQ in our FAQ section (two threads) for more information about how an amplifier works.

I wrote those to help explain questions like this. It should help if you want more detail, and saves me some time repeating things from prior threads :)

could you explain why the feedback would be caused by setting the gain too high on the amp? not trying to say your wrong. Just want to learn more

1: you still have a ground loop issue, and the JL is making it more apparent. or, more likely:
2: your amplifier gain is set too high, and you're getting feedback.

I previously had a noise after installing a new deck. picked up a ground loop isolator and that got rid of the engine whine noise. the other day I continued on with the upgrading process and installed new speakers. no noise from that. then pulled out the american legacy 4 channel amp and put in a JL 300/4. and the engine whine is back, although it is very quite, i can still hear it when the volume is very low. the JL is wired in the exact same as the American legacy was. why would the JL make more noise. could it be that its more sensative so it can pick up the noise easier.

I have a JL amp wiring Kit that i will be putting in next. hopefully that will help with the noise. After that, the only thing i could think is to upgrade my RCA's.

could running bigger ground cables on the battery help? or running bigger wires to the alternater help?