Gal With Horrible Rumbling Noise

I have a 1991 Chevy Cavalier with the stereo equipment listed below installed.  I had it installed two years ago, and am now hearing an intermittent rumbling noise coming through my sub.  It does not seem to matter how loud the stereo itself is turned up, and the only way to get it to stop, is to shut the power down on the reciever, or unplug the RCA's for the sub from the amp.  It was getting so bad, that I just unplugged the RCA's, and left it that way for a few months.  My 6x9's were the only speakers getting power/sound from my amp.  No noise during this time.  Two weeks ago, I plugged the RCA's for my sub back into the amp wondering what might happen.  Now it has only made the noise twice, and has only been for a second or two at a time.  It has not been so severe as to warrant shutting the system down.  When it is working without the rumbling noise, the sub/system sounds just as great as ever, and there are no other indications of a problem.  I am not sure if this has anything to do with it, but this did not start until I had the battery replaced in my car.  Like I said, this is not a new install, but people keep mentioning that my ground may be bad.  So, I wonder why I would just now be having trouble.  If you are laying face up in my trunk, you will see a ground attached on the metal in the area between the 6x9's, and one coming from the cap as well.  I am sorry if my descriptions/facts are vague.  I am trying my best based on what I know about car stereos (which is not much) to give you the best descriptions.  The guy that installed the system is excellent with this stuff, but is no longer around, and there really aren't any great stereo resources in this small town.  Any assistance you could provide would be greatly appreciated. 

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Alpine Type S 3"
Alpine Type S 6x9"
Alpine Type E 10" In a Q-Logic Ported Box
1/2 Farad Fosgate Cap
Profile Clarus 440
Panasonic Reciever

You might try replacing the RCA's for the sub.

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'85 Toy

Try to reground the system in a different spot.  Make sure you scrape away the paint, then screw it down tight.  If you have access to a star washer throw one on it will help the ground from coming loose.  Also you may check the connections at the battery to make sure they are tight. 

sounds like the gain is too high.   look on the side of the amp for an adjuster for level or gain. with a small flathead screwdriver turn it 1/8 turn counter-clockwise. or backwards of a clock. that should fix it.

To set your gains correctly you don't just guess.  Do a search in this forum for "gain" to learn how it is done right.  Secondly, you might want to make sure that all of your wires are still as tight as before.  Check the power cable and all the connections to the battery.  If that doesn't work, then might want to change your RCA cables.  There are so many things that could go wrong.

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That's my opinion. Take it, leave it, or correct me.

Hey, Pepto Bismol! Ok, Ok, what kind of cd player is this. It sounds more like a cd player issue to me. Check the ground on the cd player.

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Top Secret, I can tell you but then my wife will kill me.

 from what she described (a fluttering sound) and the fact that it's an inexpensive amp. i'd still say the gains to high. on a cheapo amp when the gain is too high it will make that sound and you can see the woofs moving in and out. it sounds like it's right on the borderline of being too high hence it happens only from time to time. thats why i reccomended i/8th of a turn down. the girl is also not a pro so i didn't recommend something involving a meter and spl meter or whatever.