I agree with Kyle. The patterns are stored as a digital program whereas the transporter is a more analogue device. The term matter to energy could refer from energy being used to assemble the atom (whether the replicators have a bank of elements they used to build or build the atom at of pure energy), this is pure guesswork, but is the only science bases strategy that may work based on the level of technology they have. This could explain why latinum cant be replicated, due to a quantum signature which the atom builders cant produce. However, theoretically replicators could work off the principles of quantum superposition, everything exiting in every place at once, and you merely control that.