I feel like something is wrong

So, I bought a new tower computer for college. I wanted something powerful enough to handle what I need done and I wanted to be able to customize it myself. Everything has been going fine and dandy. Computer takes a little while to boot and does some long system check and then runs fast and smoothly for the rest of the time. But ever since I got back, the opposite seems to be true. It is lightning fast on boot time, but skips the check (which is what I am worried about), yet insanely slow soon afterwards when windows comes onscreen.

It used to say "PCX-E61: Media Test Failure, check cable," I read some forums saying how to fix that and now that is gone, but it still doesn't do the check. It just kind of stops at "verifying pool data" for a while and then moves on. My computer still works and runs Windows 7 just fine (kind of), but it still raises some concerns.

My computer is an iBuyPower HORUS series rig with a Gigabyte DX10 AM3+ motherboard using AMD 760G chipset.

Thanks in advance.