He mentioned that they had different system zone codes, and that he had different RF systems in the different rooms indicating the presence of multiple processors and there for there must be a seperate file for each room , I believe anyway, since you can only have one processor in each file.

This is a real stumper. Could it be that the owner had moved one remote to anitrt room by accident? I can't think of another reason. Unless they got onto the same channel some how but based in the OP that's not the case.