You know, I've always been impressed that you actually have boundaries. I've never been good at that, and certainly not at enforcing those I make. About the closest I come is to let her know when I begin to feel uncomfortable with a situation. I believe it's a little less confrontational that telling her I'd rather she doesn't do something (but I have done that in the past) and frames it more from what I need, my desires, than from sounding insistant and controlling.
In tend to agree with Andy "Something like, "I know that nothing's going on, but I can't shake the bad feelings." This tells him you have an issue, and that it's your issue, and allows him an opportunity to attempt to calm your concerns.
