Question from new ATV user ref DVD menus

Hi just got a new ATV and installed ATV Flash. Have all my DVD’s ripped to an external drive using DVD Decrypter (win 7), all the files are in their own directory straight from DVD decripter. On 99% of my DVD’s they play fine BUT I have to manually select each VOB file or start with the first one. The problem is none of the DVD menu’s work this way, so I cant select audio set up or chapters or in case of music DVD’s i cant select individual tracks.
However one of my DVD’s has put all the files in to two directorys named audio_TS and Video_TS…this DVD plays straight away and allows selection of menus with ATV remote. All dvd’s were decripted using same package (DVD Decripter) and I dont know why only one DVD has used the _TS directories BUT its the only one that works perfectly. As I am new to all this can someone help me?? (and fix so all work with menus)