Ah... my bad I thought this was a question about using the guest script manager. Not enough coffee. You might take a look at that utility. Its great for taking the overhead out of managing these tasks. I've used it for years and love it. You can grab it from here Guest script manager package - Samples - VMware {code} .
Did you verify running a simple command works? I'm wondering if you are hitting a chicken/egg thing with UAC. If when the guest tools kicks up the command and its not already in an administrative context that might cause some issues with various commands.