@littleghost
Thanks that is exactly what it was! Who would of thought duplicate sid would work fine on Exchange 2010 but not on SP1.... I could of sworn I had run sysprep on that VM but checked with psgetsid and sure enough it was the same.
Just to clarify the work around for the EMC issue with Get-LogonUser I did was as follows:
Rebuilt my VM, syspreped it to give it a new SID (You could use newsid) renamed the server with the same name joined it to the domain and ran setup.com /mode:recoverserver on the SP1 install.
After it recovered and rebooted EMC was available however I have new issues to resolve now... ahhh I love SP1...
Credit goes to littlehost for spotting the duplicate sids.