Ubuntu – What does the Ubuntu Firefox Modifications extension to firefox do

With your old profile, could you simply disable all extensions and see if the problem goes away? (Somewhat like the safe mode you already tried.) Then, re-enable one extension at a time and see. (Obviously, the global menu bar extension shouldn't be disabled.)

If it's just a single extension (instead of some tricky "synergism"), you may be able to pin-point which one this way and then decide if you can live without it or have to endure the novelty of a centered global menu.

This appears to be a bug with the GTK3 theme, probably Firefox is using the wrong theme information for the pop-ups and the scroll bar.

I partially fixed this for myself by switching the theme for just Firefox:

GTK_THEME=radiance firefox

You can add this "permanently" by editing the launcher file:

sudo gedit /usr/bin/firefox

and adding the line (after #!/bin/sh):

export GTK_THEME=radiance

It'd probably be a good idea to file a bug against this, but now that I've finally gotten rid of the awful dark menus I'm less motivated to find the root cause of the problem ;)