So, after installing an external drive tonight and playing around with some stuff, I found that my internal Western Digital caviar black is not aligned properly in my Windows 7 box. I know the root cause of the problem was cloning the disk from the Seagate that I used to have to this WD Caviar black.
The drive itself is a WD1001FALS-00K1B0, so it's not an advanced format drive.
I'd like to fix the alignment with the least amount of effort possible. I think my best bet is to backup the 600G of stuff off that drive onto my external drive, then delete the partition, create a new one within Windows 7 and then copy the data back. Does that sound right?