At some point (around expansion 4, I believe), they decided to make the backs of one of the two types of cards lighter.
Apparently people had problems distinguishing between doors and treasures in the original releases.
As reprints of old expansions and the base game has been made, they have gotten the same treatment.
Given that people are encouraged to mix different versions of Munchkin (with different backs) and that there's even a Munchkin Blender set (with its own unique backs) I don't think this is considered a problem by most players. There are so many different cards that it's not likely you can engage in any sort of "card counting" or the like and even if you did. it probably would make a difference (considering the overall chaos level). My Munchkin set is all mixed up with the different backs and I haven't noticed it making any difference in play.