I've been working on getting CD up to version 3.6.x of vBulletin. Once that happens, the reputation box is an Ajax control, rather than a pop-up browser window, so this problem will go away. When will I be done upgrading? Who knows. I've been pretty busy these past few weeks, but things are getting under control.
If you want to poke around in vBulletin 3.6 .. check out
http://beta.chiefdelphi.com/ -- lots of stuff is broken, still, though (CD-Media, Events, Swap, etc., especially).