Yeah, it seems those doors have a one-time use for some reason. Same with routez. The secret doors only work once, and if you don't get out before they close, you're stuck.
Edit: Ok, I've figured out what the problem is. The door was checking to see if it was exactly where it started before it would open again (I guess so it won't start the opening sequence over and over). For some reason, it was ending up a fraction of a unit off at the end, so it would think it was already opening, and never open again. This should be fixed for the next release. I also discovered another bug - the secret doors will destroy equipment instead of sending it home like the normal doors do.