When an application is minimized to the tray, if you set that application (probably the default behavior for new program, I'm not sure) to "Hide icon and notifications" or to "Only show notifications", the icon is hidden and you have to use the little arrow (on the left of the tray) to display those hidden icons.
Also, can you enter this in an editbox :
//.timer 1 2 noop $!input(mIRC is not freezing!,ao) | showmirc -t
and wait 2 seconds, you should see an input request dialog, if so, the above case apply and mIRC isn't vanishing