The 12 disc sets are the original releases, they have a copyright of 2001 on them. As far as I can tell, the only difference is the lack of the bonus disc 13 in the newer sets but maybe someone can confirm if the episodes are the same or not in both sets
I received the same set. It's 12 discs but doesn't contain the 13th bonus disk. This set is an older pressing (2004 I think). whereas the newer set has the seasons broken out into their own cases, Shout did the same thing with the Bob Newhart Show reissue issuing them by season in the box...