Can you walk on the terrain? by proxy, clicking a piece beyond it and the characters automatically use it? Do you see the location icon when you click to walk on the terrain even though it doesn't work?
This sounds very similar to a problem I had converting Dunamis to the EE.
Huge potential roadblock averted. Everything was going swimmingly in the editor so I loaded up Dunamis in the game proper only to find that I Couldn't walk on ANY terrain. Click left just moved my character in a single direction.
At first I thought this might be relating to some sort of scripting differences between classic and the EE I missed in a sweep causing the problem.
But after some trial and error I noticed that certain patches of my land I could walk on but some I could not.
I have 6 pieces of terrain in Dunamis and 005 and 006 worked. I remembered that I did some smoothing on those pieces in the EE editor so I checked in the Mods\Dunamis_GUID\Levels\LEVEL NAME\Terrains folder and found that 005 and 006 had a new file called Terrain_005.bullet in addition to the normal file.
So I figured that those files had to be generated by my edits. So I simply went to each offending terrain and did a minor edit like raising the height of a small piece, saved them, and now all the terrain works fine for walking.
The problem is obviously slightly different, but those bullet files seem to cause issues like this in game but not in editor.
I'd try stuff like deleting them and regenerating those files by making an unnoticeable edit to that terrain piece and saving them.
