Could it be that Chrome updated itself and changed information in the %APPDATA% after updating itself?
When you install Chrome base it enables all kinds of update processes. It has 2 tasks it enables to update and 2 services it uses to update. It also creates en update folder where the application is installed. We don't see this issue popping up with our writables and Chrome installed in base.
We found out that it is even easier to do this without the hazard of human failure if you update or recreate the appstack.
Just download the ADMX template for Google Chrome's business edition and make sure to disable all update options. This way if a user tries to update anything it won't work.
Issue is that even if you do remove the services a user can still go to settings in Chrome itself and then go to the update tab. If the folder update exists it will just update.