TrainFX is not an infallible system, and with everything, GIGO; sometimes it gets lost when the GPS link is lost, some trains never had GPS installed in the first place, some carriages get out if sync with the others, some systems run ahead of themselves when the train hasn't even moved, some services never have a code created in the first place, some don't like it if the driver and the guard attempt to set up the route at both ends, some reject valid route codes, some don't handle request stops or short platforms.
Generally, a full master reset by tripping the MCB of each carriage is needed once in a while when digital Doris goes off on one is sufficient but all in all it's bloody infuriating when it goes wrong that it can be more trouble than it's worth.