Putting back in the stock drives worked, so I guess I'll grab some other drives. I was using Western Digital drives, any suggestions on what should work? I don't want to buy hard drives from apple due to their markup.
This is not the answer you want.
Having done driver-level and diagnostic-level device implementation, integration and development, I've always viewed the extra costs that are involved here for the vendor's core designated peripherals as paying for the assurance that the devices will work in the system, and will continue to work going forward. If you don't want to pay Apple, find another vendor that sells (and that has a reputation for supporting) after-market disk drives for your Xserve box.
Sure, there's a profit in there for the vendor. But how much does your time and effort and testing cost you? The device SCSI and ATAPI and firmware interfaces are more ugly than most folks appreciate. Yes, most devices on the market are compliant with standards, but there's nothing that requires a particular sequence or return code or otherwise. Things get particularly ugly when you get to looking at the S.M.A.R.T. data.
I've hit significant differences from one revision of disk drive firmware to the next, and this from reputable manufacturers. Usually better. Sometimes worse. In a couple of cases, I've met two completely different devices that have the same product name, too; the vendor shifted suppliers, but didn't shift product names. Or cases where firmware version 3, 4 and 5, that are older than version 2.
I'm not making this stuff up, either. It's
completely nuts. It's a testament to the guys that have designed and implemented and tested the drivers that random stuff even mostly works as well as it does, too.