I have a hotrod se. It works fine using the Mess Gui with almost everything. However the A7800 does not recognize it. When I tab into the menu "in-game" I can set up the joystick to work but the buttons will not work. Button 1 player one on the Hotrod is left alt as I remember. when I try to map to this it gives me leftalt-rghtalt

Have you tried enabling the HotRodSE layout? In MESSGUI, go to Options->Default System Options, Controllers, and then select HotRodSE instead of Standard as the default layout.

You may have to reset the drivers you use to the default settings before this takes effect (right-click on driver, Properties, Advanced, Restore Default Settings).

if the emulation is paused then mapping anything to the alt key will produce leftalt-rightalt. it's because mame/mess switches to using standard windows key presses when paused but direct input at all other times.

maybe the new ui always does it, switching back to the classic mame style might help.

smf