Is it possible that you are playing tighter to make sure you make the cash?
The only other thought i had was that at the stage you are going out the blinds will be very big and only the players with monster stacks will go deeper in the tourny. Even starting with 1,000 chips, with 5,000 players there are 5 million chips in play, when only 200 players remain the average stack will be 25,000, by the time 100 players are left it will have doubled to 50,000. If the bubble is around the 200 player mark, when the bubble bursts all the short stacks who have been folding to the money will push with rags and be eaten up quickly by the loose calling big stacks, so the average stack will raise very quickly. The blinds will also be big at this stage so if you have an average sized stack and go card dead for a time you will quickly find yourself with a short stack.