All resources PEP service owner should receive notification
A service automatically sends notifications to all of the account owner's connected resources (subject to notification filtering).
The 'send last published items' implementation in Openfire currently only evaluates explicit subscribers. As the owner is not one of those, its +notification service discovery flag gets ignored, preventing a notification to be sent.
When iterating over affiliations when sending other notifications (such as deletion events), the owner affiliation is evaluated. It does not appear to be copying the notifications to all connected resources though.
I suspect that the lack of proper distribution of published PEP items (to other resources of the owner) is what is introducing problems where clients seem to 'overwrite' rather than 'augment' each-others bookmarks.