In the tools menu it's listing the same extension twice? It should not do that. Please try changing either show versions or show icons. That should remove and recreate the menu. Once that's done please check again. If there are still two listings, are they identical (have version numbers and/or icons)? Also, can you check the Add-ons manager and make sure there aren't two listings for Extension Options Menu (I don't remember changing ID's, but it could have happened.)
As I remember: in previous versions the EOM's tools menu item replaces the default "Add-ons" item, like in the Firefox button.
In current version i have the default "Add-ons" item (button) and a sub-menu labeled "Extension Options" (just after the default "Options" Firefox item).
So, no problem with ID's, no are 2 versions installed together, EOM is working fine, as we can see in the overlays files, this behavior is totally normal.
PS: maybe i am wrong and remembered behavior of another similar extension (EM Button or EM Extensions or something like that)
Sorry for inconvenience and for very bad Spanglish.