I had a similar problem a few months back. I know you said you've checked the ground, but check it again. My ground wire broke partially at the strut mount nut and was only allowing an intermittent strong ground. The rest of the time, it was only partially grounded. What gauge power and ground wires are you using? Also, where is the amp located? Is it smothered or is it out where it can breathe easily?
Like Mr Book said, you may end up having to increase the sub output at the HU and turn the gain down to about half if nothing else is awry.
