Is "File not found" logged after the rewrite log entries in the error.log? You should be able to verify whether that file exists or not.
It does looks like that the rewrite rule has been executed properly. If you can get to the maintenance page with "/system/maintenance.html" then you should get that page when you access "/".
I think maybe Capistrano replaced the document root during the update, so "/system/maintenance.html" does not exist. However, in the manually crafted test environment, it should work fine.