i had a similar problem with my 12" mapex pro-m tom. like sabe said the 12" tom has to sound like a 12". once i figured out how to tune the drum, now it sounds great. in addition, i also got my tom cut 2 inches from a 10x12 to 8x12 as well as having my bearing edges recut to a double 45 cut, all thanks to precision drum company which helped as well....
you may want to check your hardware. sometimes tom mount issues can give you two totally different tones when a tom is mounted or not mounted.