Those problems are what I was talking about in my last post. The 3D-to-2D transitions use zoom tubes to force the player into the plane of the 2D section. Because of a change in the way zoom tubes work in recent updates of 2.1, the player is immediately sucked into the zoom tube that leads back out of the 2D section after entering it, and then back into the entrance tube after exiting it, trapping them in an endless loop. After messing around in Zone Builder, I don't think that this problem can be solved just by changing a few linedef flags or moving a few waypoints, so it might take me some time to fix it.