The autolock On / Off buttons create a database entry/option that is either On or Off. The coding check that processes the part of the function that autolocks your root .htaccess file looks for "if autolock is not set to Off". If autolock is set to On or if no database entry/option exists then the root .htaccess file is automatically locked during BPS upgrades.
Something is breaking/interfering/preventing autolock from working on ONLY YOUR WEBSITES.
autolock works perfectly on all my testing sites and the 100,000's of other WordPress websites with BPS installed on them.