While hanging out at the Money Tree at The Spot, I noticed that my watch I recently made was no longer updating. I normally don't receive money from the money tree and ignore its notifications. However, as soon as I dismissed the interrupt window, my watch started to update again.
This means the interrupt window system (Window.alert, Window.confirm, and possibly Window.prompt) HALTS all timer based events until it is cleared. This is a TERRIBLE design idea! Only the script that made the notification should be interrupted. Please do not effect TimeOuts or Intervals when interrupt windows are activated!