I've been having problems, too. Only mine are - I can add and analyze in my Collection, however when I drag and copy them to a playlist, entirely different tracks show up. (Watch: http://www.youtube.com/watch?v=QD_upB8Msn0 ) I've spent more time trying to figure out Rekordbox the past month than I have with my CDJs.
I've described my full issue here of all the fun I have been having with Rekordbox: http://houseofebonyandivory.com/2011/09/rekordbox-woes-and-issues/