If you check the first link in the original post I made:
http://i47.tinypic.com/2jd14sw.jpg . I was pretty sure that was the issue.
I blocked that IP-range from being loaded and never had another popup that day. Not sure how they get in, but I read of a vbulletin XSS issue a while back. Usually if someone were able to get into a server then they would had done more damage than this.
Google will clear itself after everything is cleaned up. A lot of it is a waiting game it seems,
http://support.google.com/weBathmateasters/bin/answer.py?hl=en&answer=168328