How did you rip them...are they .iso's?
That's where I'd be looking to first as well.
Menus are part of the rip (or not). If you use JR to rip the DVD, it rips the whole thing. If you used, say, Handbrake, then it will strip the menus / special features etc.
If they are still in their VIDEO_TS, AUDIO_TS folder format, they may or may not include menus, depending on the options you chose when you ripped them.