I have noticed a problem with mimizing mIRC to the system tray. When you do a Minimize all windows / show desktop.
[Windows Key] + D

mIRC does not move into the System Tray like it should. Doesn't seem to hurt anything, just open back up and re-minimize by using the window mimize button in the upper right hand coner, and it moves in to the system tray again.

I think that's just the way the Windows "Show Desktop" explorer command works. It overrides any "custom" minimization options (such as mIRC has) and uses the Windows default, which is to send it to the taskbar.