It very well could be a BIOS bug, I'd suggest you update to the very latest final or latest beta (Suggested)
Your RAID array will be fine, just be sure after you flash and then load optimized that you save/apply then reboot BACK to the BIOS first before windows. Then set your RAID enabled, reboot to BIOS once again and then go into advanced BIOS page and into Hard Disk Boot Priority, and then move your array to the top of that list.
Once all updated you can then try to move your array to the 6Gb/s ports, make a backup first though just in case there is something wrong with your 0 6Gb/s port. Did you try it by itself with a single drive to check if it's even working at all?