Thanks! I forgot to remove the -gen, -32x and -scd command lines, but I never thought of running Gens in compatibility mode.
A lot of people also tell me to use Kega Fusion, but I only use it when I need it. Because of the menu's, configs and some extra features, people can't really change my mind.
The version I used was "Gens-GS r7 - SonMP3 Edition" and was last updated in 2010. You must've downloaded an older version, but it still worked.