Do you see anything in the VSE log files, that the Access Protection is blocking things? Try to disable Access Protection. You may need to check the UAC Settings, as these could cause a lot of problems by installing software in general.
Thanks speter, I should really have thought to check that. When I checked the AccessProtectionLog I noticed that the windows TrustedInstaller was being blocked by an Access Protection Rule : "Anti-Virus Standard Protection:Prevent Windows Process spoofing"
I added an exception in ePO and it looks like it's done the trick. Thx again.