My experience was always that browser shortcuts took precedence over the GTK emacs keybindings. Ctrl+W always closed windows rather than deleting a word, for instance. Is it possible that you've also moved to Firefox 4, and that's added new shortcuts?
The real problem is that there's a fundamental collision between emacs shortcuts (which use ctrl) and the shortcuts now used in most applications (also using ctrl nowadays). Which should take precedence? If it's the application then emacs keybindings will often invoke unexpected behaviour. If it's the gtk widget then application shortcuts will stop working just because your input focus happens to be a text box at the time. Both of these are problems, and nobody's been able to come up with a clean solution as yet.