Here are the base specs for the system:
Motherboard: ASUS P86-M
BIOS Version: 6702 x64
CPU: Intel Xeon E3122
RAM: 8GB ECC
SATA chipset: C204 or LSI (set via physical jumper)
A little history of the system: The ram and cpu were pulled from a decommissioned dell poweredge server that had some issues. I was able to get this asus board pretty cheap and its matx form factor made it easier to find a compatible compact rack chassis. The bios doesn't have an option to load a raid configuration utility without a physical jumper setting on the motherboard. I currently have it set to use the intel sata controller vs the onboard LSI controller. The intel controller is controlled by software in windows (obviously its not running). It does support raid 5, which i was mistaken. The LSI controller does not support RAID 5. I've had on board raid controllers fail so I don't like using them. The BIOS can be set (when using the Intel controller) to DISABLED, IDE, AHCI (current) or RAID.
As far as OMV seeing it as a raid controller, maybe, I don't know. I know, at this point, the RAID 5 configuration is working. It seems to be a software issue as to why its not starting correctly. After everything, I ran sudo mdadm --manage /dev/md127 --run and the array showed up in the web gui, I mounted it and all the data was there, as if nothing happened. I had reinstalled OMV so I had to recreate my shares and users. I attempted to add the AUTOSTART to mdadm but I'm not having any luck after reboots. I would prefer to not wipe the drives. I can switch the bios to RAID and it seems to boot the same in OMV. I dont have a lot of experience with linux so i'm not real familiar with the commands or what some of the processes are. I only get to learn when there's a problem like this. Other than that, it sits in a rack with only power and ethernet.