I'm not too sure if it's the same as the problem I had, but have you checked the Normals?
I had some where they weren't all facing the same direction and that happened, or if you started with a cylinder, did you delete the history?
If neither of those are it I hope someone else comes to your rescue, or you manage to work it out.
It's looking good so far, I like the spiral tubes for travel between decks, nice idea!

Good luck!

Actually I'm not sure either of those things are right, that only happens when you are extruding and rotating at the same time, sorry if I wasted your time...