Honestly, unless you have a reason to suggest that he is hooking up with her why is it that big of an issue? People have Co-ed roommates all the time, and if you trust your boyfriend enough it shouldn't really be an issue.
I think the bigger issue that's there is that if you don't have a reason to claim that he is cheating on you, you trust him enough that he wouldn't cheat on you, then what is the real reason behind you not wanting her there?
Just something i'd look into on my end personally if I was in your shoes is what the reason for the emotions you are feeling are. I have lived with all men before myself and there were never issues with the girlfriends (one was my brother - so obvious reasons there, but the other person was not related to me whatsoever)
I think the flirtatious thing - some people do it on purpose, and some it is just a part of their personality. If you have no reason for her not to be around one thing I would suggest is talking to her - letting her know that she comes off very flirtatious with your boyfriend and it makes you extremely uncomfortable - that if she would try her best not to be that way with him specifically.