The changes made for T6799: Kleopatra configuration files in wrong places have broken the migration of the group config because Kleopatra now looks in the wrong place for the old group config. Instead of looking in %LOCALAPPDATA% Kleopatra now looks in %GNUPGHOME%/kleopatra for the old group config (which is also the new location).
This happens only on Windows (because we use %GNUPGHOME%/kleopatra only on Windows).
To test this move kleopatragroupsrc from %GNUPGHOME%/kleopatra to %LOCALAPPDATA%. If migration works then Kleopatra will copy the group config file from %LOCALAPPDATA% to %GNUPGHOME%/kleopatra.