mIRC's timestamp feature uses the formatting parameters from $asctime() identifier (/help $asctime), and there are no identifiers for milliseconds. Actually, there are no identifiers that can return the current time in milliseconds.

Ping and timers can use milliseconds only because they compute the DIFFERENCE between two moments in time expressed in milliseconds - actually, in "ticks" elapsed since the computer was started. But $ticks in itself has no meaning, as it didn't have a precise reference point; only difference between two values of $ticks is useful, to accurately determine the duration of a process.

Out of curiosity, what do you need such a high precision timestamping for? How is it useful to you, considering how many other factors can influence the delay of messages appearing on your screen, like lag and even processor load that slows down refreshing mIRC windows?