Attach a copy of your script so we can look at it and see what can be modified to get around the problem.
I recently had similar problems with unit movements and I overcame those using playmoves to force them to go exactly where I wanted them to go (within a playmove of the desired postition). Anyway, this experience made me very good at using playmove to get units to do/go where I want, so maybe I could help you by applying this to your script.
Also, I have a general script I made that uses playmoves to move an array of units through a series of positions using playmoves you determine. I am attaching that script. Keep in mind, however, that while a unit is moving via a playmove loop, that unit will be unable to do other things (like defend himself if he is shot at).