[Gandalf Parker]

Yes, thats the order of it.
The game saves the .2h file just as it would for sending to a server (or pbem).
Then any pre-exec orders are carried out.
Then the game hosts creating your new turn file.
Then any post-exec is carried out
(I know I over explained but some lurkers might suddenly see why those are handy)

I know of no way to stop the flash of jumping to the command window to run the bat. I usually run Dom3 in windowed full-screen mode because I play lots of large map solo games. I like to see the tabs of other things I have going on so I can easily jump in and out of other programs.