Windows hides icons that are sent to the tray. mIRC has an option to either send it to the tray or not. Previously, the default was to send it to the tray. The setting has been changed so it defaults to not send it to the tray. This is because Windows will hide the icon by default and then new users have trouble finding the program to open it back up. With this change, anyone who purposely changes the setting will know that it's in the tray and where to find it and those who don't know about that option won't get lost.
You can enable it again in Alt-O > Other > Tray, if I remember the location correctly. I may be incorrect on the exact location as I can't look right now, but it's near the bottom and it's a button marked Tray.