Sorry, I've been quite absent from the forum lately as I've been busy outside. I still haven't got the time to look into this but it sounds to me like this makes sense:
The RDP server has its own username and password that you can set. It would be a very bad idea, security-wise, to give away the administrator's password to anyone who needs to connect remotely to this machine.
You did all the work! 
If the problem is on the remote host, the server you're connecting to, then I would expect the issue to persist. But I don't think it would share the same settings either way. The Gnome shell used to power the desktop environment has its own internal drivers for networking; A separate third-party client would likely use its own settings.
Did you restore to a previous snapshot through Timeshift, maybe?
For SMB, I would recommend setting an entry in the /etc/fstab file which controls the rules for mounting drives, partitions and network shares. You can see an example in the thread below, where you can create a file with the credentials to use, which shouldn't be overwritten by any update or anything.