It is hard to tell without seeing it and testing myself. There has to be something in the stereo wrong because if you remove the fuse your drain disappears. I would have to think one of your power wires on the back of the deck are hooked up wrong. I know on the back of the deck there is a constant for the memory, one for when the truck is started to tell it to turn on, and one to dim when the headlight go on. So my first check would be to make sure that the remote wire from your amp is not on the constant power. the amp would be on but you may not know it because of no signal to the sub would not hum or anything with a good system.
Or maybe you have a bad ground someplace. Electrical problems are hard to find when they are not in front of you. I am an electrician and I have to chase bad connections all the time.
Good luck. Sometime the answer takes awhile, while other times it just pops out of nowhere!!!