Uploaded file versions appear as unrelated changes after server upgrade

After a server upgrade from 8.1.8100 to 10.0.10000 to 12.3.12304, the reviews that were active before the upgrade can no longer be updated as expected. New file versions that are uploaded by a svn diff from the GUI client or by direct upload from the web browser create a new set of changes that seem to be unrelated to the previous versions of the same files. The "View as: Overlay/Separate" toggle-button is grayed out.

New reviews created after the upgrade do not exhibit the same behavior and work as expected.