Well like the what the others sayd, could be a signal that you PSU is going bad. But if you dont agree..
Try this:
1. place the GPU in the other slot (8x) not the (16x) and do several boots. If that solved it its your mobo. If not...
2. Try the GPU in a friends computer and boot up some times. Same problem thats the GPU gone bad.
3. If it works at a friends PC, but not in yours, its 1 out of 2. Mobo or PSU. Borrow or buy a new PSU to check.
Oh and dont tell me that you have forgotten to say: Oh and by the way I have like 30 HDD`s running of a 550watts PSU... cause I have seen someone do that.....