I had similar problems with this. Then I tried to test the tutorial and the standard files and came up with a basic template for a map and a non-crashing dungeon.
Download my template in this link and replace with your own map and proper names in the dat files accordingly: viewtopic.php?f=28&t=11075&p=102743#p102743
It should work fine. Don't forget to place a "starting position" layout link timeline, (and probably an exit). TBH I forgot what was it that made my map crash. Not exactly sure at this time of the day ^_^ sorry. If it doesn't work I'll try to remember.
In any case, exclude any triple-way chunks, or four-way chunks, those are absolute crashers.