Hi,
Are you loading projects made with older versions? Old projects don't have some of the new data like palette or dithering (they do have emitters position though).
I've just tested it with the latest version and emitters position, palette and dithering seem to be workin fine, I can save it, close the program, open it, load the .ppd and the values are restored. Excluded colors are not saved, I forgot about that.