I have to agree with cyberbillp. Not just about the update, but MediaBox in general. I'm guessing the only reason there isn't more talk about it is because most people, like me, are simply happily using it and it works nicely.
I Uninstalled and re-installed it. Thsi time the first time I scrolled in the Media Directories window, all the pre-configured directories disappeared. I added my own, refreshed, and they have been there ever since. There still seems to be a bug of some sort with the media preferences and adding directories, but at least this time my custom additions stuck.
BTW the /Music. /Images, and /Video directories are on my Removable 4GB SDHC if that might help with anything.
Using MediaBox is pretty intuitive, but still I came across the walkthrough and thought it was pretty cool.