The tray seems to blink when any traffic is sent or received from mIRC, which I feel is a greater indication of the server being 'alive' than if it only blinked for user messages and the like, of course that is just personal preference.
An option to flash the 'i' and 'r' letters via a script, which would work even if the animate tray option was disabled, would allow you to customise the behaviour. You can already blink the entire icon with /flash.