I managed to isolate the problem a little more:
*edit*
Pressing the binoculars or attack/observation periscope icon or F3/o causes the problem
(from that point on mappingrooms/icons/menu bar are messed up, especially crewmanagment. The radioroom and some other rooms are still ok, though.).
Pressing the flakgun/deckgun icon or F11/F10 fixes the problem (crewmanagment and mappingrooms are ok again). :hmm:
So it seems that stations where 2D and 3D are combined, will cause problems.

Please confirm.
By the way, I also tried a 'menu bar'-mod. Well... that didn't worked either.