5D Mark III HSS Problem in Low light

We have a somewhat serious problem with our two Mark III's...or some obscure setting.  
When the light level get's too low, they over expose when HSS is on. We can slow down the shutter so it turns HSS off and everthing is perfect. But, once you speed up so HSS is on, it is way over exposed (about two stops). This happens with both cameras and an ST-E3-RT, a 600EX-RT and/or a 430EX - off-camera or on. It doesn't seem to matter what ISO setting or exposure setting, once it goes below a certain light level it over exposes. We are normally around ISO 10,000, F2.8, 1/250. At this point, flash compensation has no effect, camera exposure compensation does change it but then you can't go back to regular light levels or no flash without switching it back. Another hint is that I can change the off-camera 600EX-RT compensation on the flash itself and that will help. But again, if it goes back to regular flash, it'll be too dark.
So, there is a clear difference in exposure between HSS and regular, or no flash at low light levels.
We've used this method with the original 5D and the 5D Mark II and all was fine. This is new with the Mark III. 
It is possible we have some obscure setting incorrect...hopefully. Any help would be greatly appreciated!

mortontd wrote:
We have a somewhat serious problem with our two Mark III's...or some obscure setting.  
When the light level get's too low, they over expose when HSS is on. We can slow down the shutter so it turns HSS off and everthing is perfect. But, once you speed up so HSS is on, it is way over exposed (about two stops). This happens with both cameras and an ST-E3-RT, a 600EX-RT and/or a 430EX - off-camera or on. It doesn't seem to matter what ISO setting or exposure setting, once it goes below a certain light level it over exposes. We are normally around ISO 10,000, F2.8, 1/250. At this point, flash compensation has no effect, camera exposure compensation does change it but then you can't go back to regular light levels or no flash without switching it back. Another hint is that I can change the off-camera 600EX-RT compensation on the flash itself and that will help. But again, if it goes back to regular flash, it'll be too dark.
So, there is a clear difference in exposure between HSS and regular, or no flash at low light levels.
We've used this method with the original 5D and the 5D Mark II and all was fine. This is new with the Mark III. 
It is possible we have some obscure setting incorrect...hopefully. Any help would be greatly appreciated!
There's definitely something wonky about this situation.  If anything, the photo should be DARKER when using HSS.  And flash compensation has no effect, but exposure compensation does?  That doesn't make much sense with regard to the flash power.  Exposure compensation should have no effect on the flash at all if you're shooting in Av mode.
Try shooting in manual, and do a "factory reset" of your camera body and reset all custom functions.  

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