Some games of mine have minor freezing every so often

Here's some background about my issue. I have Windows installed on an SSD, but most of my games are on my secondary storage device, an HDD. Every so often in only a few games (Mainly AC3 and Shadow of Mordor), usually during cutscenes especially in Shadow of Mordor, it will freeze everything for about 5 seconds while continuing to play the audio (wherever the audio left off.)

Then, after that, during live gameplay it will do the same thing. I can't quite figure out why, and here's what I've done so far:

• My paging file was off. I have since turned it on, both drives, but allocated more to the HDD (about 5GB.) The SDD has about 1GB. This didn't fix my problem.
• I have a gaming laptop with two GTX 980 (not M) graphics cards in SLI. Perhaps SLI is causing these freezes?
• In power management, I turned off "turn off HDD after a certain time to conserve power." No luck here either.

I'm out of ideas here. I would move the games to my SSD, but I have uninstalled them because frankly I was annoyed. If it helps, I stored some music on my HDD and the same thing happened. I'd play it, but then they'd freeze for a while and pick up. Perhaps my HDD is damaged in some way? That would be a bummer because this is a brand new laptop.