Does it boot into safe mode? (You do know how to get to safe mode, right?)
It could always be that you just have bad hardware. I run linux, and as such, have no need to ever reboot. One day I decided to, just for the hell of it. When I did, the computer would no longer boot. As it turns out, somewhere along the line, something toasted both my motherboard and video card. (They're dead as disco. I have an identical machine which I played the hardware swapping with, and it confirmed both motherboard and video card are toast. The really odd part is the video card, since it was working seemingly perfectly, but now no computer with it in it will remain stable.)
Now the interesting part here is that linux ran just fine, until I rebooted. Then because it needed to access or check some nifty piece of hardware apparently called apparently at boot, but no place else, it couldn't boot any more.
At any rate, the moral of the story is, never reboot your linux box because you don't need to.