I tried burning another DVD but that did the same. The original install I did worked fine.
I remembered I had a spare 250GB SATA2 drive at home from a failed pair in a RAID0 array. I disconnected the two drives in the RAID0 array and hooked up the single drive, changed the BIOS to SATA/IDE and rebooted. After formating the 250GB drive the install went fine with no issues at all.
It appears to be something to do with the RAID function. It is working fine with Vista on the first partition but when the server goes on the second it is having a problem. I have updated the BIOS to latest and that did not fix it either.
I know how to get around it now but am still worried I might have a hardware issue that is waiting to bite me.