If the MPFS tool works with the Explorer 16 and MCHPBOARD hostname, then be advised that Windows caches hostname resolutions. I believe the cache expires after 10 minutes. In other words, if you try successfully uploading to your Explorer 16 and then in under 10 minutes, try uploading to your custom hardware (also using the MCHPBOARD default hostname), then the PC will automatically attempt to access the old IP address that your Explorer 16 was using, not the new IP address that your custom board is using.
To clear the Windows hostname cache so that you can immediately swap boards without the 10 minute delay, open a console with Administrative privileges and execute the command "nbtstat -R". You also could probably disable the network adapter and then reenable it to clear the cache.
If you changed your hostname to something other than "MCHPBOARD" on your custom board, then that's possibly your problem. You also would need to change the path in the MPFS tool accordingly when swapping boards.