It is very rare that there are problems between the HDD and motherboard. Yes, I would say that If you did a clean install, it would fix your issue. Just make sure that during setup, you do not select the 'Upgrade' option, and do a custom install instead. When you get to the window asking for where to install, click on the hard drive and click 'Format'. This will wipe your drive and get rid of any bad sectors or stubborn files.
Let me know how you go!