I second (or third now?) raise my hand for HDD issue. I guarantee you their "checking the HDD" was to look for SMART errors and if no alerts fired it was just passed on. Don't rely on their warranty service to do formal diagnostics; a lot of warranty replacement places have a set script to follow as far as diagnosis and I'd say 15-20% of the techs don't think outside the box. Prime example is the new Geek Squad at Best Buy. When they were their own company they were awesome, and when I was working as a black shirt on the tech bench at BBY they were great too. But after the merge corporate pushed all of the techs to start pushing sales instead of true fixes, and for years they languished in incompetence.

Anyway, I digress. You can get a 2nd HDD for dirt cheap from a lot of places. Just image it real quick and see if you still have the same issue. The issues you describe are textbook HDD I/O issues and 90% of the time it's evidence of a failing HDD. The other 10% is an actual bad SATA/IDE controller on the motherboard itself, which usually you can only diagnose with a 2nd hard drive anyway. Good luck and keep us posted!