XF 2.1 User still shown as having custom node permissions with all set to inherit

Do any nodes have this setting:

Private node
If selected, users will only be able to view this node if they are explicitly granted permissions.

And "Tom" is listed?

Or is Tom listed as a moderator/admin under Groups >> Staff?
 
The node isn't down as being private, and Tom is a Super Moderator, but isn't specifically a moderator for that forum. We have another forum with the exact same parent category and permissions set, and Tom isn't down as having custom user permissions like here.
 
But why would this show as a node permission? This isn't a global user permission.

We have other users also set to have moderator permissions who don't show.
 
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The 'Tom' user has custom permissions set through the 'Administrator' user group, but this doesn't explain why the user itself is being shown as having custom permissions set. There are several other users with the 'Administrator' group, none of which show.
 
This can happen if an add-on you have uninstalled left its permission entries behind.

We have a tool which should fix it. Tools > Rebuild caches > Clean up permissions.
 
I'd already ran the tool and that didn't seem to resolve the issue.

Getting some other weird behaviour as well. We have added 'sambob_12' as a node-specific moderator of a node, as shown here:
205563

But this user isn't shown as a content moderator here on the 'Moderators' page, like the other users:
205564
 
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