I have an S5000XVN/XLS Server Board in the SATA configuration. Currently there is the system drive which is plugged into SATA0. Additionally, there is a 6 drive RAID setup plugged into a AMCC/3ware 9650SE card. With this configuration, all is working as expected. I want to add an additional SATA drive (not to be part of the RAID) and am having problems doing so. When I add it into the system, the RAID stops working properly. I believe what is happening during the boot process is that the system drive (SATA 0) is initialized, followed by the new SATA drive, and then the RAID. Is there a way to have the system drive be followed by the RAID and then the new SATA drive?
The order in which drives initialize, shouldn't have any affect on a standalone RAID card.
What is the card reporting? Have you tried disabling the Option ROM for the onboard SATA, since you're not using onboard SATA RAID?