@dankcushions Do you know what's really strange? When upgrading I lost the save states from loading on mupen. But now when I copy the save files from the rom directory to the save directory under muper64plus it load the saves again!
So, two questions:
Where are the standalone mupen64plus saves and save states stored? I would say both roms/n64 and mupen64plus/saves since I backed up from roms and restored to saves, and it worked fine. IE it saves to roms/n64 and mupen64plus/saves and loads from mupen64plus/saves only.
Why do the save file and the roms file have different names? I cannot answer that. It seems like mupen recognizes the rom and saves files with a standard name.