I take it you went down the Winguides Tweal Manager route then? I would doubt this would introduce any form of malware on your PC. It looks like a respectable web site. Do you have antivirus software on the PC? This would alert you if the Tweak Manager was carrying any virus.
I also found it here :
http://downloads.theregister.co.uk/Windows/Uti lities/Optimisers/winguides.html
I implicitly trust The Register. They would never recommend anything that would cause a virus or trojan.
Me thinks your IT chap is a little paranoid... saying that, you need to be nowadays.