An add-on compatibility problem was recently discovered in Firefox 16. It is present in Firefox 16 and above, and we’re currently investigating it.
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.
At the moment we consider the impact of this bug to be fairly minor, so it won’t be fixed until Firefox 17 unless there are sufficient reasons that merit the creation of a 16.0.1 update. If your add-on is affected by it, please let us know how in the comments.