Hello and thank you for buying MuGen!
Did you try to randomize the seed?
If you change Base Key and Base Scale/Mode - is it reflected in the file name?
EDIT: I found the problem, it was missing the settings file, so either you can create a file called MuGen_prefs.json in the application directory, or you can download the updated EXE files that will instead place the configuration file in your home directory (C:/Users/NightOwl35)
Sorry for the inconvenience!