Jeff, I literally ran across this exact same thing in my own using and in the Mozillazine forums. With the help of another person we found the cause. It's a bug in TBA (*NOT* in Firefox - that's important to understand). Something about how TBE works makes it so that javascript popups - which are initiated by the user- do not work unless in "use multiple browsers normally" window mode and/or "open tabs instead of windows for new windows opened by javascript" is unchecked.
The author of TBA has been notified about this problem:
http://white.sakura.ne.jp/~piro/xul/forum/?763