Noticed this FIRST on my old Mac G4...but now that I have a pretty new MacBook Pro...I'm seeing the SAME thing!
I go to delete something from iTunes...a song, a podcast, a video file and for that menu I am in I will get that Are you sure you want to remove screen with the "Do not ask me again" check box...which I tick...then that window is followed by the keep or move to trash window. Go to delete another file and that first one doesn't come back up again.....FOR A COUPLE DAYS!
then BAM the first box pops up again and I have to hit the Do not ask me again box. I don't mind doing it ONCE for the podcast menu screen, once for the music library and then again in the movies and tv shows screens but then I DON'T think I should ever have to do it again...but I am.
SIghh...help!