The problem is the OS tells Keyboard Maestro the file is complete, even though it's not. I use a construct like this that loops until the file size stops changing:
The key part is the just the shell command that extracts the disk size. I then store than in one var, and compare it to a previous value. If they're the same, then the file is done writing. If not, update old value to new value, and test again.
-rob.