There is usuallly a red line or green line on the serial ATA/IDE cable should always be pointing to the right side. I know its obvious to some, but its one of those wires you think you can plug in either way, but you cant.
The colored line must be to the right of the slot and it should work fine.
Pretty sure this isnt the issue, but i thought i would throw it out there in case. There are instancesd where the cable can go either way, but some drives have "issues".
Barring any connection issues, i would format and reinstall the OS if your virus scanner isnt picking up any viruses and this anomoly continues.