At the end of each workday, I shut down my computer.
My instinct is to hit ⌃, ⌥, ⌘, ⏏, switch off the monitors and walk away.
However, Skype will prevent system shutdown by asking:

Of course, with all monitors switched off already, I will not notice this until the next morning and it is driving me nuts.
Do you know how to make Skype just shut down (and up) when I tell it to shut down?
Edit: I am using Skype 5.1.0.935. To reproduce, open Skype, open some conversation (double-click some contact), then quit Skype using the Dock icon or ⌘, Q.