I spent a few minute designing a dungeon, then I tested it... and it svcked balls! (as in Dwarven Spheres, ofc...)
But that's not the problem, because not only it svcks balls, but it also glitches my bonghole out of my mind.
Here's a video, if you have a fix, post it and you'll save me and everyone who had this grieving issue.
http://www.youtube.com/watch?v=b_HoCbZir0w

As you can see, at first the dungeon is fully functional (top and first room) but as soon as I reach this corridor, the whole thing is fiddledeefied into the void.

Have you used rooms? It looks like a problem with those, I've seen it for mine.

I hadn't managed to sort it yet, was just playing with it at the time. But that definitely looks like the problem I had.

Check they cover the whole room and your portals are set up right.

Also check and make sure that there aren't any gaps in between the room bounds, and that the portal is linked to both room bounds.

So simple, I shouldn't have skipped that "optimisation" class, thanks!