ground loop, pioneer avic-f90bt

Hello, I'm a newbie when it comes to car audio. I installed my 4 channel amp and speakers over 2 years ago and never had a problem. I installed my sub and amp about 6 months ago and didn't a problem until last week. The infamous "alternator whine" came on. I began to look for the problem and discovered that my ground wire came loose from the amp. (I'm guessing it's because someone kicked the amp when they were getting out of the car) So today I went to Radio Shack and bought the ground loop isolator. When I installed the ground loop isolator, the alternator whine went away but I noticed that the sound quality went down. I'm not too familiar with the term Ground Loop but would it be safe to say that I have a ground loop? If so, how do I narrow in onto the problem? Thanks

By the way, I also noticed something weird. When I don't have anything connected to the female end of the rca from there is no whine but I don't hear any lows from my speakers. However when the female end touches bare metal (ground, the speakers go back to normal. P.S. I have a Pioneer AVIC-F90BT

Thanks, I'll try this tomorrow. In addition to the problem with the RCA Shield, could there be anything else wrong with it?

If you have a Kicker amp, you may also have a blown fuse of the same type inside the amp as well.  HIGHLY UNLIKELY, but it could be possible.  Emphasis on highly unlikely. 

This is a common problem with Pioneer decks. when your amp lost it's ground connection it began looking for ground somewhere else.  It found ground through the RCA cables, this was connected to the radio, and there is a small fuse installed between that connection and the chassis of the radio.