I've never worked on a server before, but I would imagine the troubleshooting techniques are probably the same.
- Confirm the BIOS was properly updated and it was the version needed for v2 compatability
- Are there any additional requirements needed by the new processor? I'm speculating, but are there additional hardware requirements, or perhaps power needs?
- Have you checked out the Xeon Specification update white paper?
- A BIOS update typically reverts the system to default settings. Is there a setting that needs to be adjusted?
I know the last one always gets me - especially if I'm running a RAID (the update clears the RAID settings and I end up seeing "Found New Hardware" when I boot up. D'OH!)
Hope this helps.