It could be that some brushes intersect in a strange way.
Examine Crash000.log
There may be things like:
Brush 1764 (face 1)
If there are lots of entries for the same face and brush then that could be the cause of the problem.
Make sure you don't have any cuboid brushes that are rotated by a multiple of 90. As well as being a possible cause of this sort of error, that sort of rotation is unnecessary and quite sloppy.
In Dromed use the command hilight_brush 1764 to find that brush. Note that the brush number is the 'Time' value +1
It's not always easy to see a highlighted terrain brush so you can select any brush with a similar Time and use Tab/Shift-Tab to cycle to the correct one.