I have a similar issue, but i have found a workaround to it. Apparently Theater Mode being gone from the menu is the result of Cyano Media Downloader being enabled at the same time as Theater Mode (though i can't remember the bug happening initially when i installed Cyano Media Downloader). Once i disable Cyano Media Downloader under Preferences / Plugins and then restart MusicBee, Theater Mode is shown again in the Menu, but disappears again after enabling the other plugin. I'm not sure if there could be other causes for the problem, but probably this helps solving it.