@ Tina – Actually not so wierd. If you were installing BPS Pro 12.3 then the BPS Pro code that was in use while you were doing the installation would still have been 12.2 code since 12.3 code did not exist yet until after it was installed. I assume the AFS cron code in BPS Pro 12.3 kicked in after BPS Pro 12.3 was installed and automatically did whatever was necessary to fix whatever issue/problem occurred previously.
There is still one odd issue occurring with the WP upgrader_post_install filter that we are looking into, but it only applies in this exact scenario: WP Automatic Update: WP Core, Plugins and Themes Automatic Updates are set to autoupdate and multiple pending plugin or theme updates are available and a WP Core update is also available. It seems that even though the WP upgrader_post_install filter is returning data, the process of doing multiple Automatic Updates is somehow not continuing beyond the first pending Automatic Update. Note: This issue/problem does not have anything to do WP Shiny Updates: clicking any button or link to update or install WP Core, Plugins or Themes.
AutoRestore Automation Fine-tuning:
ARQ Status Check: Core check that checks if ARQ is turned On or Off prior to Shiny Updates. If ARQ is turned Off then ARQ will not be automatically turned On. This check is specifically related to the scenario where someone has manually turned ARQ Off and does not apply to ARQ Automation automatically turning ARQ On and Off during automated installations and updates, such as WP Automatic Updates.
AFS Cron: ARQ FailSafe Cron job that automatically turns ARQ back On if the upgrader_pre_install filter turns ARQ Off, but the WP Automatic Update does not complete or is aborted and ARQ is not turned back On in the upgrader_post_install filter. ARQ automated file backup is performed before turning ARQ back On as a failsafe, whether or not the WP Automatic Update actually completed successfully or not.
BugFix: Performing a Plugin or Theme Bulk update on the WordPress Updates page: AutoRestore (ARQ) Automatic Shutdown & Backup Notice displayed and ARQ Bulk Update trigger was not turning ARQ Off. WP 4.6 is scheduled to be released on August 16, 2016. BPS Pro 12+ uses ARQ AJAX Automation for WP 4.6+ versions. The BPS Pro 12.3 fix for the Plugin or Theme Bulk Update only applies to WP versions below 4.6. BPS Pro 12+ ARQ Automation is conditional based on the WP version that is installed (forward|backward compatibility).