Dawg,
The only suggestion I could give is to try another controller, I have two and they get beat up pretty bad and are still working fine, I also have the PS3 remote which is BT, I have not experienced the problem you discribe, like I said if you can get another known working controller and see if that works, if not it has to be in the Ps3 console, but I highly doubt that, just try another contoller, this will at least narrow your culprit to the machine or your controller, since you already tried the controller wired, I don't believe it is the PS3. Hope this helps.
Jeff