How often do you use a program, decide to take an action (I.e. Press Return), and then have something popup and use your action before you even have a chance to read the popup? I hate when that happens because I don’t even know what I told the computer to do.
Input on a new UI element should be disabled for a short time to ensure that the user actually wants to take action on the new UI element. The delay has to be just long enough for the user to realize that the action may do something differently and not too long to slow down users who know that the popup is coming. So the delay should probably be a few hundred milliseconds.