Okay well I spent an hour or so scanning for malicious stuff, I did come across some high level threats (I swear to god I don't go to shady sites, I'm not that kind of idiot). Anyways those are cleaned up, did the scan in safe mode with Microsoft Security Essentials. Gonna wait a while to see if I get anymore of the same pop-up. Funny thing is, it goes away by itself if I move the mouse. Anyways if that doesnt work I'll try disabling java in startup and install javaRA.