When I imported my old game from MM2, I lost all items any of my chars had equipped. (Items that were not equipped transferred just fine.)
I then went back to my save from MM2 just before the finish, unequipped everything, saved the game and imported again. Now I have all my items.
But it's a bit strange anyway.
(MM2 was downloaded from bigfishgames, MM3 from here. But there shouldn't be any issues with incompatibility, should there?)