PS: It might be caused by the repositories, even the KNIME Partner Update Repository, not being updated. After adjusting the repositories many new updates were recognized.
did you use the workspace with the 5.3 RC and then with 5.2 again afterwards?
The reason I am asking this is that I am currently tracking down exactly what you are seeing. I observed duplicate and non-updated/inconsistent update sites after I updated a freshly downloaded 5.2 to 5.3, re-used the workspace with a fresh 5.2 instance again, and then with the 5.3 again. In my case, I had the “analytics-platform” update site twice (5.2 and 5.3), and the rest were 5.2 update sites.
I am sorry for the trouble and glad to hear that you could fix it by cleaning up the update sites.