(Note: This problem was discussed via Chat with Atlassian Support today. Atlassian were going to create a ticket for it but it seems they may not have done that yet. Problem initially related to numerous plugins including the Adaptavist Community Bubbles (CB) plugin. Guy Fraser from Adaptavist also has a comment on this system problem which I will add to this issue.)
That is, the repository is not correctly showing that new plugins are available for all relevant plugins it lists. In this case, the new CB 1.1rc1 plugin is listed but there is no upgrade link. And, the only way to upgrade this plugin (and some others too) via the repository is to first uninstall the plugin and then reinstall it (1.1rc1 is then the version that is listed for installation).
Atlassian said that it may have something to do with metadata being upload or not by developers but I think something else might be broken in the PR plugin itself.