I just got to try out the latest version, 0.9.2, and thank you, things are working great. I usually store all my funscripts in a seperate directory, and I specified the directory in the configuration. If the funscript have any special characters in the name like & or () it won't load them, but if the funscript is in the same directory they load fine.
Also, will it check directories recursively? I haven't had a chance to try that yet.