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.
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: