Are you willing to leave him because if my girlfriend (don't have a current girlfriend) ever did that, that would be the end of that relationship, plain and simple.
Who knows what else he put on there and even if you scanned with every spyware scanner and virus scanner and keylogger scanner in the world that would still not guarantee 100% removal so your best option is (if you think he has done something else) to format your drive and reinstall Windows. I didn't say it was easy, I said it was the BEST option, in this case.
I find myself asking this question, don't answer it but ask yourself, did you ever do anything to warrant this type of observation? Not that you did and not that you didn't but I don't have the advantage of his perspective as well. I'm not going to go there, I think I'm just going to stop talking now.