Hrmmm I haven't run into any problems myself with it still choosing from all folders. I say just try saving the settings again and see if that works. It is supposed to only pick from your selected folders. If you have NO selected folders, it loads up all your bookmarks.

I do plan on rebuilding it eventually though to optimize it better. This was my first addon i've built.

I'll also have to look into launching an addon from the desktop, i've never tried that myself. Sorry.