Good detective work and glad you figured it out!

Looking back, it seems like v3 didn't require '--super'.
Presumably, since v3 used a custom/hacked Perl version of rsync on the
server side, Craig had coded the functionality of '--super' into the
Perl code.

David Heap via BackupPC-users wrote at about 09:29:50 +0000 on Thursday, March 
16, 2023:
 > Resolved, thank you to everyone who replied.
 > 
 > > What transport protocol are you using?
 > > Can you reproduce this when the file is moved elsewhere?
 > 
 > These pointed me in the right direction, thanks - I copied the folder to a 
 > new location and all the files were backed up as root:root. Having a further 
 > look around this and other backups it appeared that anything with a ctime 
 > after we upgraded from BackupPC v3 to v4 a while back wasn't getting the 
 > correct ownership. Anything with a ctime before the upgrade was fine, even 
 > if the contents/mtime was updated afterwards.
 > 
 > It looks like the rsync arguments we used on v3 did not include --super for 
 > some reason, which is required for --owner to work. I think we let BackupPC 
 > upgrade our config file but we don't have the upgrade logs any longer to 
 > confirm. It looks like it was never added to the command for v4 so rsync has 
 > been unable to transfer ownership info for new files. I'm not sure how it 
 > worked on v3  but I'm just glad it's working now we've added --super into 
 > the arguments.
 > 
 > Initial full-server restore tests after the upgrade worked fine as all the 
 > service files existed pre-upgrade and kept the correct ownership. It's taken 
 > a while for a new file to be involved enough in booting/service startup to 
 > flag up the issue.
 > 
 > Thanks,
 > David
 > 
 > 
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