Stereo & Electronics - engine feedback noise

I am coming across an intermittent feedback in my stereo. it sounds like the noise a bad ground will give ya. but heres the thing it only happens when its cold. is that a common thing? here is my stereo setup

clarion dxz945mp
front- jbl gt636 series 3 ways
rear-focal 6 1/2's
rear amp memphis 100 watt amp
front amp same as above
sub alpine type r 12
powered by a Memphis 500d

also there is a second battery for the stereo complete with an isolator. all wires are run correctly IE power runs along the opposite side of the car from rca's.

the noise happened a few days ago but I was having (car) battery issues. charged the battery later that day no noise. I leave work this morning and the noise is back. both batteries are seeing 14 volts (separate gauges) when running and both batteries are holding 12 volts.

amps are grounded to the seat belt mounts (upper rear) via the proper connectors. nothing in the stereo has been changed in months.

thanks for the help

Just curious, do you have the battery + terminals tied together? If not, do it and see if that helps. If you have different voltages (during charge or not) you might get that noise.

I have a battery isolator so the batteries are not connected at all

Ok I missed that, sorry. So then connect them, to make sure they have exactly the same voltage. Being that they share the GND I would be curious to see if that helps.

Also, (I'm curious) how do you charge the battery(ies)? Do you have a switch? I'm not familiar with exactly how an isolator works.

how an isolator works is that it has an input from the alternator and a power on wire.it also has two separate power posts for the batteries. it allows both batteries to be charged but doesn't allow one to drain the other.

both batteries do not share the same grounds. one is in the stock location one is in the rear drivers side.

I have 2 separate voltage gauges. auto meter for stereo battery and stock for stock battery.The second battery is grounded to the rear seatbelt bolt and the amps are grounded to the battery.

OK, Thanks for the info on the isolator. I wish I had any other ideas to throw out. I get a little feedback too, and only once in a while. I wonder if they are the same.

yeah the only thing that is going to make this hard to diagnose is that it only happens when its cold. I leave work at 430-530 am and thats the only time i hear it.I live about 7-8 miles from work and it goes away about half way home.I will talk to a local shop and let you know what they say about mine