I have an MSI 785G-E53 motherboard with an on board AMD SB710 5 port SATA II controller that supports RAID. When I am running the controller in IDE mode my SATA DVD drive is listed in the BIOS as the number 1 SATA device under Standard CMOS Features and all my programs that run outside Windows can see the SATA DVD drive and work with it with no problems.
When I put the SATA controller in RAID mode the DVD drive is no longer listed as the first SATA device nor does it appear anywhere in the IDE list under Standard CMOS Features. It know appears on the boot menu where you access the RAID console but the DVD drive does not appear anywhere in the RAID console itself. None of my programs that run outside Windows are now able to see the SATA DVD drive but Windows can and use it with no problem.
Next I plugged the SATA DVD drive into a 40 pin IDE connector on the motherboard using a SATA to IDE bridge and in RAID mode my programs that run outside Windows can see and work with the SATA drive with no problems.
How many SATA ports do you have on your board? and how mann of those ports are RAID enabled? Generally its only 2? Please get back to me as maybe its just changing of the sata port you using? You could have the drive plugged into a raid configured sata port