I figured out what is going on.
step 1) The pre-command is setting up the u360s with the desired configuration
step 2) fat fingers is not finding the game in it's database (games.dat or whatever it is that states what each game is such as 4way) and defaults to analog. So it configs the u360 as analog
step 3) The Genesis emulator starts
step 4) The genesis emulator exits
step 5) fat fingers runs (sets u360 to Mala config)
step 6) post-command runs (sets u360 to Mala config)
The fix is to disable fatfingers unless you are using mame. I could swear that this is possible.
Having said this I did find a workaround on the internet (probably here). Don't use pre/post commands. And start the emulator from a bat file that runs the the u360 configuration files prior to running the exe.
Need to find the link to the resolution that I found.
I might tryt this tongiht granted it is not my desired solution.
EDIT:
Thread with bat file fix:
http://forum.arcadecontrols.com/index.php?topic=80546.0