the DOS games apply their own, additional computation regarding mouse position, speed, acceleration and so on.

dosbox tells it exactly where your stylus went/is, but the games interpret that differently, they make it go further a few pixels so it seems smoother. (considering the quality of ball mice back then not a bad idea actually *g*).

but dosbox cannot know that of course, because it only "feeds" the difference to your stylus' last exact position to the game.
which now differs from the position of the cursor. this adds up over time, resulting in desynchronization.

(feel free to correct me if i understood it wrong )