I am having the same issue. The file is written in the EEPROM of the Pluto as I can re-open it and see my changes. But upon reboot those files seem to be replaced with a copy of the unmodified version of the file. I'm also having an issue updating firmware as well by putting a copy of the updated firmware in this directory. It is supposed to see a new firmware and begin the update process. This too fails.
I don't see that anyone has found a resolution, so I was just asking again to be sure.
Thank you so much.
SOLVED:
apparently the trick is to EJECT the Pluto based drive after editing the CONFIG file and writing to it. Once I did an EJECT it worked perfectly!
I suspected it to be a WINDOWS issue and this procedure made it work.