First, the checkboxes under options are not remembered. I have to uncheck the box replace existing playlists with the same name each and every time I do the feature. This is particularly annoying because of problem #2...
...which is the fact that if that box is checked, playlists are replaced even if they don't share the same name. For example... say I am exporting a playlist of 3 star rated files, 4 star rated files, and 5 star rated files to iTunes. If I export the 3 star rated ones and 4 star rated ones they go into a folder called Media Center and then are named 3 stars, and 4 stars respectively in iTunes. However, if I then export the 5 star playlist but forget to uncheck the box (which should remember my settings and be unchecked automatically), then after export, the 5 star playlist will be there, but the 3 and 4 star playlists will be removed even though they don't share the same name as the 5 star playlist (only the same folder).
