I've heard this before about the 48" MOD deck. I am not sure what would cause such a huge difference in performance from the 54" or 60" MOD decks. I have the 60" MOD and while I am not a fan of it at all, it doesn't have any of the problems you mentioned.
Make sure all the linkage that opens and closes the baffles underneath are connected and working correctly. If you don't need to truly mulch with it very often, then remove the two adjustable/removable baffles at the rear in between the blades on each side to open the deck up some. It makes a big difference with mine. The way they come from the factory is really too tight for side discharging unless the grass is thin and/or short. If you're using Gator type blades of any kind, get rid of them and go back to OEM high lifts, or if you mulch a lot of the time, get the OEM wavy mulcher blades. They work 10 times better for mulching the any other blade you can stick under the deck.