MultiFE is actuelly designed to use with a 4 button neogeo layout which have all colored buttons, that hence I use the top toolbar to tell what they does (hence they are RED, YELLOW, GREEN and BLUE, colors that can been changed on the toolbar). These four buttons is the 4 fire buttons MAME use by default too. I called them Action Buttons, simple because they are dynamic change what they really do, where you are in the list or you example using the Search, Song Queue, games etc. The toolbar is the heart in MultiFE and hence I can't use 5 and 1 this time, otherwise MultiFE would just been another typical FE with same controls. MultiFE was pastly a Jukebox software, before it went to a Frontend.
For launching game, I need to checkout the multife.log, so I can see what it happens, if you actually have the game. Yes, it show all games in list from the XML, until you click on Optimize Database, which clean up all games you doesn't have controls for and also checked if the rom is in the roms dir. In next version I think this should done automatic after creating database to remove missing roms.
For the Jukebox I think you is using Singles which is do that way by default, but it have many configuration on that (MultiFE was a Jukebox application only in the past).
NB. For refreshing a library is done if you do something changed when hiding the config or by pressing F5 (Refresh). I think it was documented? There is no need for a Save here, due it normally do that automatic.