Hard to say without sitting in front of the system. Unless you have production data on the disks, deleting the configuration and re-doing it from scratch might help. Anyway, I don't think this will solve the boot issue. I rather think (unless it's an issue with the CDROM itself) it could be related to a BIOS setting where you define the boot controllers, i.e. the CDROM is likely not connected to the RAID controller, but another e.g. on-board controller.
André