I think I know the pleat/crease that you're referring to... The Red leather seems to be one of the softer ones too, so the crease falling out might just be due to the softness of the leather. Are you using it regularly? If so, perhaps you could just try "resting" it for awhile and storing it back in its dustbag flat, rearranging the middle pleats as much as possible, and putting a light weight on it (maybe one massmarket paperback book) to try to create the crease again.
The middle pleats/creases aren't supposed to be as defined as the side ones, though. It's just supposed to be a pleat that starts from the top then gradually evens out as it gets to the bottom. This may also be why the pleat/crease is falling out on your Jovi, if you've been using it for awhile. I think storing it for a bit with something to "squash" the pleat/crease back into place (but nothing too heavy!!) should help, though, but this is just a guess on my part. HTH!
Oh, and like LR mentioned, the pleats/creases definitely show up to varying degrees when the bag is in different leathers. The Bordeaux and Oceano Soleils, for instance, virtually have no creases, due to the wrinkled texture of those leathers! I think the Fall '09 Jovis were all in fairly soft leathers, though, so whilst that means that the creases are fairly defined at first, there might also be a higher risk of the creases falling out eventually due to said softness. Some of the Holiday '09 leathers are more glazed than the earlier Jovi leathers too, so those might be stiffer and less prone to having the crease fall out. (I haven't seen any Holiday '09 Jovis in person, though.)