Glad you got it working.
My 2 cents:
No action button, joystick, coin or start button should be a shift button, or combo with any other of same buttons, for menu, exit, pause, etc. Never ever. For the exact reasons you found out (the hard way).
Others here seem to have no problems, but IMO one problem is far too many in something that can be prevented with an extra "config only" button, or keyboard like you've done (wireless might be easier).