Hein's problem was that he deleted all the wav files from the mpqs and
instead placed them on the Starcraft folder. SF would crash when
trying to read the wav files to play sounds. I suppose that's not your
case (you have not deleted anything from the mpqs, have you?). I also
have no idea why it wasn't display the "File not found" exception and
displayed a runtime error instead.
Also can you check if setting the units in transit crashes? Make a new
map, place a terran building and set it in transit. If it doesn't
crash can you make a copy of your map, delete all the units with other
editor then try to load it with SF. Does it crash?