Current SVN, recently compiled maps in the April 26 2007 GTK 1.5, using the UFO2MAP currently available.
Stairways with space beneath them appear to be failing on all maps. See below screenshots for examples. farm08d and italy05d confirmed failures. ALL stairways with 'gaps' below show this problem. (Example, stairway on italy05 that goes up the sides, that doesn't have space under, work just fine).
As far as I can tell, the cause is the stepon brush (at least for one of the maps I looked at, farm08). See below.
The stepon brush neither allows the character to walk high enough to reach the next level. The other 'internal' stairway in the farmhouse shows a similar issue.
The internal stairway in Italy05d.map, however, does NOT show a similar problem. However, the actorclip surrounding the stairway at the top is being ignored (allowing you to step through it and fall to the lower level). It also has a similar problem as shown in the screenshots above of not allowing you to walk back up.