Post description already explains, but in some seeds room106 and room079 overlap, causing collision/visual bugs. This happens for example, in world seed "123123" (though I don't know how to upload saves)
Easiest way to reproduce:
-create world with seed "123123"
-teleport to "room106" or "room079" via console

+1 to this. Also happened on two different seeds of mine (one of which has had its game deleted), "fz06va" is the one I still have. I only remember the other seed was 4 characters. As it usually happens to me, the collisions manifest in the following behaviors:

• Attempting to enter the stairwell of 079's containment will drop the player outside of 106's "house,"usually in the corner furthest from the steps down from the control room.
  
  If the above doesn't happen, approaching the halfway point of the "airlock" room before 079's containment chamber will cause the player to either drop through the map or end up on the staircase at the entrance to 106's chamber.
  
  Trying to leave 106's chamber after having set foot in the main part of the room can teleport the player into 079's chamber. Event flags will not trigger, so 079 will not speak to you and you cannot open the door out.
  
  Even assuming all of that doesn't occur every time, the framerate chugs, especially from shadows trying their damnedest to draw correctly and failing. Approximately 200 MB of physical memory can be eaten up by that alone.

Thanks for addendum Torcularis, I forgot to mention a similar issue of "teleporting around" between their two chambers. However, a fix for the close-spawn issue should be expected to fix other issues such as these.

The problem, as it appears to me, is that the rooms spawn diagonally from one another; on the s-nav for instance, they appear corner-to-corner, implying that some anti-overlap checking should be enhanced, as the rooms (or at least room106) is/are bigger than 1x1. Good luck devs!

Can confirm.