I'll bet you're shooting wireless, right? If so, the problem is that the wireless unit you're using can't synch faster. This is why I never wanted to go with the older pocket wizards--they only syched at 1/160th.
I had that problem with a cheapo wireless. It wouldn't sych any faster than 1/200 on a 20D I had. In the beginning it would, but for some reason, with use, it got slower.
I can confirm that both my 5D and 1DSMKIII do synch at their specified speeds using the new Alien Bees wireless flash units.
If wireless is your problem, try using a PC cord to confirm that, since the cord will have not have problems that a wireless might have.