What a day! We think we have finally fixed the root problem by slightly repackaging one of the plug-ins. The change is on the update site, and the issue should no longer occur (at least it doesn’t for us).
Apologies for the problems and frustration this caused. We do have automated and manual tests that verify the update of older KNIME installations. However, as far as we can tell, this problem has only surfaced (a) on Windows and (b) only when a certain set of extensions was previously installed in 5.4 or older.
– Bernd (+ team)