Ok, you are trying to watch the VIDEO_TS media folder back through DVD Player then, right? Sorry, but as stated in DVD Player Help:
"You cannot add bookmarks or video clips to movies that are played from DVD Media folders. Video folders from DVD discs with copy protection cannot be copied and played from your hard disk."
Sorry, it doesn't sound like there is a solution for this! Although I believe that last statement is incorrect because you are able to watch it through DVD Player, just not create bookmarks or video clips. As a half-substitute, I believe the VLC media player can play back VIDEO_TS and create bookmarks, but I don't think it has Video Clip support.