MacBook Pro Audio Jack Delay
I have a very similar issue on my 2012 retina display MacBook Pro.  Since the latest update 10.9.4 there has been a delay in the volume adjustments for both the speakers and headphone jack when using the volume buttons on the keyboard. The delay is of 3 or 4 seconds. I can bypass this delay using the volume adjustment on my menu bar at the top right of my screen.