help you fix your problem You miss a - to start the second application definition in your YAML. Without it, there is one single item in your list where the latest attributes overrides the first (duplicate) ones:
Hope that helps If I understand the question correctly, the problem is caused by the fact the logger itself has a log level, not just handlers. Logger's log level defaults to WARNING, which seems to be set on your logger. If a generated message has a lower priority than the logger's level then it does not even make to the handlers. So try setting logger's level to DEBUG. info_file_handler should ignore any messages more verbose than it's own level.
Config Yaml to run PHP and Python with AJAX in the same project with App engine