The same thing happened on the PC when I upgraded to 9.0.25.
It did not happen the first time I opened WL after the update but the second time I opened WL all the plugins were re-scanned and the preferences were put back to factory settings. It is strange that both the PC and Mac versions did this exact same behavior. This is not normally the way WL updates behave. I did not have the “re-scan plugins” box checked when I restarted WL.