So right now I have stella running at 640x480 and exiting every time to MaLa with the layout not jumbled. I am not using a delay in closemul nor do I have Reorder layout checked and I do not have a momentary jumble.

I have rebooted many times and changed emus and run different games, each time no jumble at all. I am afraid to do more testing since it works. May ghost it as it stands first.
I think I did figure out why the launcherres needs to be set to 800x600 (or whatever your windows res is) though. When I was testing the closemul quit delay I noticed Stella closed then the launcher was open for a second then it closed. The launcher is the last thing open before Stella shuts down. So possibly changing the resolution 3 times (stella to launcher to MaLa) may have been an issue.

I am letting closemul handle the exit and not stella or MaLa
So here is my setting right now:
MaLa: Stella emu kicks off closemul, command line "%path%\%rom%.%ext%", no hotkey used, and Reorder layout after game quit
is not checked
Closemul.ini: Exit Key=27, Program=stella.exe, Quit Management=7, nothing else set.
Stella.ini: video=soft (not using openGL), fullscreen=1,fullres=640x480,center=1,launcherres=800x600
Windows resolution = 800x600