Not sure if it applies in this situation, but have you tried, while mIRC is the active window, to hold down the CONTROL-BREAK keys? In case a script has somehow gotten into an infinite loop. It's hard to tell if you've reached the ON START event when a script could be causing this.
I had a problem where mIRC would have a LONG pause every time I started it up, though it would continue on after about a minute. It was happening during the period while scripts were executing the ON START event. Finally I traced it to a script that was only setting and unsetting a few variables during ON START. When I unloaded that script, suddenly no more pause. I renamed the script, then copied back to the original filename, and reloaded the script-copy using the original filename, and when I reloaded it there was no more long pause.
I've had disks where a bad sector caused the accessing application to freeze for long periods, but not sure if it'd cause a delay as long as you're experiencing.