I'll try to explain what happened. I had transfered some files onto one of my hard drives via usb, then I attached it to my system via one of my SATA ports. Everything was fine. Then I had plugged another drive to one of my SATA ports to create a RAID1 array. However, Intel Matrix Storage Manager seemed to think that the second (blank) drive was the correct one, and it seem to want to try to rebuild a RAID1 array with nothing on it.
Now, I stopped the whole process and ran CHKDSK. Now, none of the files appear on the single drive, however, when I right-click on the drive in My Computer, it says that it is nearly full (which is what it should be). I just can't see any files in it.