The problem you have described does not seem to be an issue with Intel® Rapid Storage, at this stage, try updating RAID BIOS or option ROM (OROM), make sure to contact MSI and get an updated BIOS with OROM updated.
Then try again, if the problem remains, it could be an issue with the on board RAID controller.
FIXED - Ended up reflashing the BIOS, which restored the RAID utility. BTW, my G15 keyboard would not register the CTRL-I to get into the utility... I had to use a PS/2 keyboard, which required a CMOS reset in order to recognize. Just posting this in case anyone else runs into this.
Normally, you can't just change to RAID mode from IDE or AHCI even with Intel's AHCI/RAID driver installed, on an OS installation that was not done in RAID mode. The usual result of doing that is a BSOD on reboot. Check this link for more information:
Thanks parsec, I already knew that... I was actually trying to make a fresh install but couldn't get the RAID working... I just mentioned that it was working in AHCI and IDE modes to show my HDD and Windows were working OK. Thanks for the help though. :-)