Error connecting through SSH Tunnel

[J Sovreign]

I have a php web application (Server A) that accesses MySQL on a remote server (Server B) through an SSH tunnel. Once the tunnel is set up, I can log in and run queries on Server B from Server A exactly as you would expect. However, when the web application tries to query the server I get the error:

[PDOException] SQLSTATE[HY000] [3159] Connections using insecure transport are prohibited while --require_secure_transport=ON.

Sure enough if I set the require_secure_transport system variable to OFF, it all works as expected but I do not understand why the web application connection triggers this exception but a normal connection does not.