Server 2008 R2 boot drive letter changed

I have a Windows Server 2008 R2 running on VMWare ESX 4.0. The server
was running fine for months, then after a reboot, the C drive has been
assigned to the 100MB System Recovery partition, and not Volume 2
which is where the actual OS sits. I have attempted to rebuilt the
BCD, I have attempted to use diskpart to manually assign the drive
letters, but every time I restart the vm the drive letters reset to
the System Restore as C, and the OS partition as D and the result is a
blue screen because the os files are not found.