SSD HDD Combo problem?

I wonder if your hard drive goes to sleep. You can try leaving your power options for the hard drive disk to never sleep.

I have all hibernation/sleep settings shut off. This kept happening with Diablo 3 so I said screw it and installed it on my SSD and no problems. Only when it's updating files on the HDD. Also, I have both drives set on AHCI. Is that okay?

Yes, it's perfectly fine. Assuming your hard drive disk is SATA. What kind of HDD is it? Brand and Model.

Western Digital Caviar Blue WD10EALX 1TB 7200 RPM SATA 6.0Gb/s 3.5" Internal Hard Drive

Does this only happen with WoW?

It happened with the Diablo 3 updater as well... Oops maybe this isn't a drive a problem... either way I'm not sure what direction to go from... the downloader is running right now so I'll see if it freezes while I'm doing stuff. It always freezes while I'm away.

Okay, my best advice is to talk to tech support regarding the updater problems.

Here's an update:
The WoW launcher would keep freezing my computer after so long of time. I did a hard restart many times because of it. Now when I start the launcher it immediately goes to a World of Warcraft Optimization window. Because it's having problems with info on my drive? It says "The Launcher is optimizing your World of Warcraft install. This is a process we run from time to time to improve game performance and reduce the size of the install on your hard drive.
Then the bar says "Reconfiguring game files. Please wait." Then my computer completely freezes. Every time. Even in safe mode with networking. This is a newly built computer. Brand new hard drive. Confusing  

Problem solved. The hard drive had bad sectors. Since I'm new to building pc's I didn't know what bad sectors meant. Now I do. Newegg is replacing free of charge. They wanted me to pay 13 bucks for a return shipping label which was b.s. I chatted with an extremely nice customer service representative online and she sent me the label for free. Let's hope the next drive works.