[Zubersoft]

Anytime you change the settings and exit the settings screen, it saves all of the preferences to files that are stored in the private application data directory. Some settings immediately are changed and written to the file when you change them. So you definitely should not be having to do that each time. What pedal actions are you selecting? It might be worth having you backup your library under Settings->Backup and Restore->Backup Library, uninstall MobileSheetsPro, reinstall it, then restore the settings and see if this problem persists. 

Mike