Thanks for your PM. As I only have a super admin logon what I will do if it is OK with you would be to install Akeeba and take a copy of your site to work on locally. I am off to bed now so it would be sometime tomorrow that I get a chance to do this. I am sure this problem isn't too urgent as it is more of a admin issue.
I tried usink Akeeba to backup your site but it seems to not work only getting to 266kb so I was unable to download it and try anything.
I am guessing that when you do a discover that the script is still finding some xml files and those are what you are seeing but without access I cannot check. I will however try to replicate on my local system.
It seems that as well as some DB entries in your case there were also a couple of XML files hanging around. When I remove them the J updater didn;t give those entries. Personally I would not worry about it.