The reason for the differences in caliber nomenclature is simply put, bore diameter vs. groove diameter. A 31 bore is a 32 groove; a 36 bore is a 38 groove; and a 44 bore is a 45 groove. This is a carryover from muzzleloaders, which are measured in bore diameter to breech-loaders, which are measured in groove diameter. Cap and ball Colts might best be described in this context as "transition" pieces.
J.L.