A new version was released with fixes people wanted 🙂 Have fun here are the details.

It fixes the problems people had with selecting a ROM file using the joypad. (thanks to Tortri for the quick testing) The bug only showed up if the root directory of your CD had less than 15 or so files. Now it works with any CD. Also long filenames have been reported to work correctly. NO spaces in them, though.
Ngine Snes9x 0.30a (Disk Juggler) (Self Boot)