ok, this time i got something new: engineer1 does not get listed anymore (but is running), while engineer2 is still ok. as both are running on the same server, same user, even same gamedata just with different setting files, this was probably not from a network issue but in internal bug.
the last logged thing is the shutdown of the server after a game with only one faction was played, which ended instantly. maybe the masterserver does not accept a new game directly after one was just set to "in progress"?