I don't see any way to respond to a timeout issue if Facebook is down or not responding when I use FB.init. There's no option here: http://wiki.developers.facebook.com/index.php/JS%5FAPI%5FM%5FFB.Bootstrap.Init%5F2
Would be nice if there were some way to respond to errors like you can with normal xmlhttprequests. Is there such a thing with Facebook Connect?