I couldn't take it anymore and pushed the dreaded reset button. And it worked! It only picked up everything in the room. The three rooms connected to the command deck had closed doors and were not affected. Now, I'm sure the bridge deck will pick up not only the bridge but the elevator room, hall to officer deck, and escape pod area. But, it seems that the closed doors do work on the guildship as a buffer to the reset button.

I use that trick a lot. The problem is that if you can't select the hook, you can't pick up the deco or change the arrangement. I'm having the same problem. Underlurker on a single medium tile. Can't even find a tiny edge of the hook to select and get rid of it. So, I'm just sitting here staring at the reset button. I just don't want to loose the three rooms I just finished on the Command Deck of the guildship (I'm working on the center room). Or worse, the entire ship.....

It also does not seem to be linked to the 100% Voss planetary achievement. Just got that last week and no luck. Not sure what other Voss achievement is left after that.