Amp always unless deck is offand sub makes constant thumping noise

I have a system installed in my pick up. I had installed it in the summer and everything worked fine for 5-6 months. All of a sudden the deck cut out and i shut it off. Left it off for an hour or so and then turned it back on. Ever since then my directed 350D amp remains on unless i turn the deck off. Not long after my amp kept feeding my sub what sound like road noise even when the vehicle wasn't running. That has changed to a constant thump noise that is very quick and is continous. I have all new cables except my positive charge from the battery and my input. The thumping seems to cut in and out but not totally fixed. I have everything secured very well. I haven't changed the ground for my deck (which is a Pioneer DEH-P4800MP) since it has been the same one for almost a year. I have not changed anything from the deck and the amp as far as adjustments since this has all started. When I turn the volume up i can drown out the thumping but the output isn't what it should be when i do that. Any help would be great.  

Check the ground from that battery to the frame, your ground there may be bad.  If there is nothing wrong with that try regrounding the head unit.  The amp will always remain on when the head unit is on because it is hooked up to the remote turn on wire on it.