In the end, there didn't seem to be an answer to this issue. It was likely caused by an import of a very old configuration file from my previous machine.
I deleted all the backup plans and made new ones. The existing backups were successfully connected to for the plans which used legacy file backup - the backups continued where they had left off. The one backup that I had set to use the new (non-legacy) file backup format wanted to backup all files again.

I tried the cloning when it first happened and the dup plan had the same issues. The plan was created with the same software (desktop/Windows) and version and on the same system. But in my long journey to move to a new system, which really has surprised me with many issues, I did do an import of a plan created by a really old version on the old system. Perhaps that's where this issue started. I will explore further or just start from scratch.
Thanks so much for the help David.

Ya, meant to include that... 7.1.3.28