Thank you for the response. Unfortunately, these are all temporary fixes. The chkdsk is definitely the quickest method, instead of going down the diskpart route. However the problem still persists on a reboot. Maybe what I'll try tonight is moving everything off the drive, running chkdsk...
So, got a new OCZ Vertex 2 120 GB over the weekend. Installed it, everything went fine. Blew away my old install (backed things up of course), loaded raid drivers during install. Formatted both, installed on SSD with my D drive as Games/Music/Etc. Now everything seemed fine on first boot...