I think that NullDevice and Und3ertak3r have given you good advice. Your problem is slightly different from the usual trojan scenario in that it was installed by someone with PHYSICAL ACCESS to your machine.

As Und3ertak3r suggests, they would probably have had to turn things off to do this.

I think that it would be wise to check ALL your AV and firewall settings to make sure that they are both properly activated. If you don't, you may be leaving yourself vulnerable to an external attack.............there is nothing like dealing with a known problem for lulling people into a false sense of security?

Cheers

EDIT: Just had a thought.............if this guy has had access to your box with full rights, who knows what else might be there...........maybe you only found what he wanted you to?.................depends how good/bad he is