In a setup with one frontend server that proxies to a backend mod_perl server, authentication should be performed entirely on one of the servers: don't mix and match frontend- and backend-based authentication for the same URI.
File-based basic authentication (performed by mod_auth) is best done on the frontend server. Only authentication implemented by mod_perl handlers, such as Apache::AuthenDBI, should be performed on the backend server. mod_proxy will proxy all authentication headers back and forth, making the frontend Apache server unaware of the authentication process.
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