The problem is sleep mode now really doesn't care whats running for applications and will suspend them, it seems to base its idle timer on direct input. I found people complaining about it on a video rendering forum where their renders where being suspended in Windows 7 and the PC was going to sleep.
I did however find a solution to my own problem, setting power options in command line using powercfg.exe. I can tell it to use the 'high performance' profile (no sleeping) through our install batch file and then reset it to use the default 'balance' profile during the sysprep script.
