I can't say for certain, but it's in fandom it's commonly said that transporters work on the quantum level, while replicators only work on the molecular level. This could lead to slight errors in replicated material, as with the replicated DNA in the TNG episode Data's Day.

The fact that latinum can't be replicated, or at least isn't economical to replicate, suggests that it can't be produced from the raw material used in common replicators (or perhaps that raw material would have to be more valuable than the latinum itself). However, it may still be possible to store it in a transporter pattern.