Sorry, they're implementing new stuff so occasionally they're coming over and changing folders that I file things in and explaining that to me, so I have to go afk for extended times while they do it :\
Anyway, yes, I see what you're saying -- particles are "made" in some reactions, but it's more ontologically complicated than that. In quantum electrodynamics for instance, the particles are always there (except not, as "virtual" particles), just some reactions make them separate from being potential to being real; but in a SENSE they were already there -- yeah, basically, quantum voodoo, I know.
Essentially this is how microwaves make the photons that heat up your food; I don't really know whether that's feasible in a replicator or not. Seems like you'd need orders of magnitude more matter to work with to MAKE matter.