From the Firefox Add-ons Blog comes this alert:

The problem is that the window load event handler that many add-ons depend on isn’t fired under some circumstances. So far it appears that this only happens when a popup window is opened, and only in cases where the domain in the new window is different from the one that opened the window. Since most add-on scripts rely on the load handler being called, many of them will not work in the newly opened popup window. There’s more information about this in bug 799348.

Depending on the scale of this issue (how many or what type of add-ons are affected) this will be patched with  Firefox 17 due out November 20th, 2012 or with a firedrill release of Firefox 16.0.1 sometime in the near future.