You might be having HD issues. Check to make sure your disk isn't full or near full. Also, if it is a slower HD 5400 and it starts writing to the outside of the disk, that could cause you issues.
I would check the HD before I started messing with anything. You can also make sure your resources aren't being over taxed (something running in the back ground) If Windows, control alt delete, task manager, more options, performance.