Its not a symptom of teh games age coupled with graphics card drivers at all as wacker says, but a well known bug since 2005, and together with the civil war bug one of the most annoying of those that were left in the game (there are many others). It was termed "dance of death" because the men kept being shot by the tower ballistas while "dancing" up and down at the base of the tower.

As you say its from large to epic stone walls only and the associated towers. There is no cure, except bringing two towers and use the otherif the first gets the bug, which might of course screw up your plans in getting the city. Just consider it as a potentiality when you attack these types of walls and plan your strategy with it in mind.