I'VE RUN INTO A PROBLEM.

I just bought a 2002 Lexus is300 and it has a factory amp.

I went to install my Pioneer Premier CD/Mp3 player, and ran all the wires correctly (I even had a professional helping me) and we ran into a situation that has us somewhat baffled right now.

We had to wire around the factory amp because we do not have the JBL wire harness that hooks up to the factory amp. Well, the CD player was working fine. All speakers were working except one rear speaker. It had them skreeching! So we didn't hook it up. It was working. About an hour later...listening to music...mid-song it skreeches in the rear again.  

So I'm thinking its either 1) a pinched wire...2) mis-wiring somewhere...3)my speakers need to be replaced or my factory amp needs to be replaced??? I mean, i dont know. Can I just use my Kenwood 800watt 4/3/2channel amp to hook up my speakers to? i have 4 left and 4 right input/outputs for speakers on my amp...but i'm trying to bypass that as a "last resort option". And, also, I was thinking...Should I just go to eBay and buy the JBL wire harness for my factory amp? It's only $89.99 ----- I just wanna know why it's skreeching like it is. Because when we tested it, it worked. Then it didn't. We took that wire off, it worked for an hour almost....Now it's not again.

Can somebody please help me out with some advice?

I'd greatly appreciate it.
Thanks guys!  

allmost sounds like a bad
ground?