Searched mantis and browsed current reports without knowticing this reported. I've only ever knowticed this in 3.0f. After being in the command chair and jumping out (haven't tested ejects for the same issue yet) the popup menu is (as far as I can tell) broken until the end of that round. It goes up properly if the popup key is depressed, but all the options but "eject commander" are greyed out and if they menu key is released the menu disappears instantantly (compared to being removed by a +attack press normally). Items are still selectable, but the popup menu key must be held until the selection is complete, and releasing the key acts as a selection rather then pressing +attack.
Extreamly annoying if you forget about it midway through the game and you have been in the command chair early on for whatever reason. I have accedentally shot the hive or alien structures several times intending to call for orders so a com could drop a PG on my location.