I have that problem too, where i delete systems i don't want, but they show up again. A simple fix is to just delete the contents of the rom folder but, leave the empty folder there. So nothing shows up the main menu now, and because the folder is still there- the system won't try to put anything back. Another bug is, deleted games STAY in the menu selection no matter what. I have to actually edit it out of the gameslist.xml to make it go away.