If I understand this right, you want the startup to be the main MAME section (All Games.mlg) first entry every time. Maybe you are saving the last emulator and game selected to be back in the startup. That's what I do.
If you do not want to save the last selected game, uncheck it in GUI-Options-Gamelist/Misc-Track selected gamelist and game.
Look at mala.ini [Starting] or [Emulator] section to see what gets called. See selection.ini to see which game is selected on startup of that gamelist. If you need to reference the emulator, find it in mala.mlt.