Pretty much what jacobhind mentioned.
The game needs to calculate lots of things: What does each lord do, where to attack, what to defend, autocalc battle outcomes, where and if new bandits spawn, etc.
Now, when you fast travel, the same amount of calculation needs to be done, but in a shorter time period. If your cpu is not done with the calculation, the game will pause/stutter to allow some scripts to finish calculating, before resuming the game. Otherwise your game would be out of sync in no time.