Well if it's the first time the table is being ran, it might just be that the dmd window is being reset. The wrapper does this for you the first time, waits a couple of secs, and then re-positions.
Generally what cause the focus issues is the front end you are using, unfortunately. Some try to force focus on the launched app and it throws everything out of whack. I haven't seen it happen when just lauching the wrapper though, so you might want to test that.