Only FMP/FMS is allowed to use port 5003, it is officially issued to FMI:
That port is hard wired into FMP and FMS so it cannot be changed. I highly doubt that something else is using it. And if it is, they should be checking that IANA list for reserved ports first...
If you find someone else using FileMaker's reserved port, it is probably because your machine has been hacked and running as a bot to be remotely controlled by a supposedly known and allowable port. Yes, a port can always be overridden and stolen by another program, but it is almost always done for nefarious reasons. Also, FileMaker does not support using other ports than the ones they have reserved. I know people have had heart burn about this as they try to work their way around firewalls. But the real answer is to get the firewalls configured to allow programs like FileMaker to use their approved ports.