Some of the nastier rootkits can actually subvert your anti-virus program and alter your Windows OS.
Can you bootup in Safe Mode and run your McAfee scanner there?
What I usually do when Im checking out a system out is bypass Windows and run an AV scanner.
A free AVG Rescue CD
lets you create a bootable 'live CD'
with an AVG scanner and a few utility tools included. As the name applies it can come in handy if you can't get the HDD to boot.
You can download and burn to a CD following the guide I linked.