Corey - I presently have my preferences set to pause the clock once the movement is accepted. I'm presently in the process of loading in a tournament that TD wasn't used for (it wasn't my turn to host). I'm declining the movements until a table collapses, but the clock still pauses.
Additional Info: Taking a closer look, it's pausing as the player movement dialogue opens - or at least a split second prior to the dialogue showing on the screen.