Sorry for the delay everyone.
bhe2g1, I can see this problem, but it is caused by AutoHide extension which inappropriately handles popupshowing event for flashgot submenu, overwriting visibility fro separators that ME has set. I have a fixed version
here. However ME 20050315 has some sort of workaround for such extensions. Thanks for figuring out precise steps to reproduce!
Shazam001, it's not that easy. UI you described would awfully hard to create or understand. So I made Menu Editor to go through items of the menu being shown and hide consecutive separators. However mostly due to conflicts with other extensions, which show/hide various menu items and separators themselves, you sometimes see the doubled-separators problem. It would be nice to sort out all these issues during testing stage (and either include some workarounds in Menu Editor or get other extensions modified to work nicely with ME), so please report all oddities you see.
thorazine, there's no hidden cache or pref, but complete reset only happens when you click Reset All or remove menuedit.rdf in your profile.
Everybody who experiences problems with separators, could you please download the latest version and report the id of the separator(s) that is misbehaving. Also, what are the nearby menu items and what needs to be done to see the problem.
Install 20050315.