The DVD's are the same IIRC, it's the packaging that is different.
I think originally a lot of box sets (Friends, B5, Buffy, X-Files etc) came in foldout packaging, when they rereleased them for budget sales they moved them over to the cheaper to produce but (in my opinion infinately better) M-Lock packaging.
I may be slightly biased though as to me M-lock cases are pretty much the best DVD case (easier to use than 90% of other hub types*), and much sturdier than foldout cardboard cases.
*Some of which either hold onto the disks so hard you almost snap them getting them out, or so loosly that the disks don't stay put.