Ground looping or bad RCA’s?

I have a 2004 wrangler and stuffed underneathe the rear seat I have a 200x2 and 75x2 PPI amps. The larger amp drives my JL sub and sounds awesome. The other amp powers my 3-way diamond set up front. Whenever I turn on the stereo there is engine noise and a high speed ticking sound. I was playing with the RCA's where they connect to the amp and found that by pushing the cables in towards the amp the clicking would go away temporarily. I have 90 degree rca adaptors hooked in as well. Both of the amps go into a common ground point on the chassis. The head unit  is grounded directly to the battery. I'm affraid that something in the RCA connection in the amp is bad because they seem a little loose. The sound in the speakers other than noise is perfect. I have been simply drowning the noise out by turning up the volume for now. The other problem I have is when I switch from the i-pod selection to the radio there is a loud pop. Any ideas on how I can fix this would be appreciated because I am totally stumped.

First, replace your RCAs.  Regardless of what problems they solve, they sound like they need to be replaced. 

Second, wait with other experimenting.  Once you have some RCAs you have confidence in, then isolating any remaining problems will be much easier.

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New Project: 2003 Pathfinder

Try grounding your RCAs.

The cables that I have going to that amp are aluminum insulated monster cable RCAs. They are for home use, but I'm pretty sure they are still good. The guy at the store said that they were top-notch cables. How likely are RCAs to go bad?

Ahh. Sorry, I misread your post. You said the RCA connections in your amp seem loose and that you are able to push them in. ---- My mistake!

Then, I would have your amp serviced. Something appears to be wrong with the RCA ins on your amplifier.

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New Project: 2003 Pathfinder