It might have something to do with the fact that your BNC (or the server) isn't replying with the correct PONG data. Typically, the computer sending the PONG is supposed to return the same data that the client is sending in its PING.

In your sample:
-> irc.inet.tele.dk PING :TIMEOUTCHECK
<- :irc.inet.tele.dk PONG irc.inet.tele.dk :heidel

mIRC is sending :TIMEOUTCHECK as its data, however the BNC/server is replying with :heidel (presumably your nickname). I imagine that mIRC sends that PING, and then sets up an internal PONG /halt for a reply that contains :TIMEOUTCHECK. Since the BNC/server isn't replying with that data, the PONG isn't being blocked by mIRC. If I am correct about this, then I doubt that Khaled will alter the behaviour of mIRC since your BNC/server isn't responding in accordance with the IRC protocol.

-genius_at_work