In some cases, the EncoderPos and FastStatus may not read back correct values for any axes other than the first axis. Checking a terminal shows that TPE returns the correct values.
This indicates an old com6srvr.exe file. A new one can be found with a new version of Motion Planner or on Compumotor's website under free software. Be sure the old com6srvr.exe is deleted before trying to replace it.