This is because you are sending PING TIMEOUTCHECK to the server, which is scripted and not mIRC's normal method.
Therefore the PONG reply is shown. You'll need to hide it with an on PONG event.
Actually mIRC sends a time-out-check on behalf of the user when it does not receive a PING request from a server for some period of time (Which was actually slightly modified in version 7.19) in order to reduce 10053 disconnects as well as to detect when you've been pinged timeout.
The BNC should be sending a ping to IRC client. This does not appear to be the case in his situation for whatever reason.
