A Small Orange responded – “Tools.php seems to exist in all the directories. I did a diff between the tools.php file for the main site and a couple of the add on domains, and it did not show any differences. I am also not seeing our scanner flagging the file.”
Tools.php exists in /wp-admin/ for all the domains, so no problem there.
The /wp-admin/bulletproof-security/ directory does not exist however, so the update process fails for the add on domains. The sidebar link dies trying to find tools.php in a subdirectory within /bulletproof-security/.
Thoughts?