I need to make some tests about this, but I highly believe that if you do this:
then do any other move, then return back to the general stack and move it, the game will act like if your stack is still in Athens. In case this is true then your sea transport probably had a very big chance of being TBED (the move in which you mixed it with your gen stack, maybe that was it's priority).
critical also suspect that there is something wrong with the "zig-zagging" and that it doesn't count as one move...