That's a *really* interesting result.
I had always assumed that the reason the high speeds only worked at small apertures with the stock software was that Canon was using a single iris as both aperture and mechanical shutter. As such, the blades have much further to travel when the aperture is wide open. I haven't taken apart the optical assembly on any of these cameras, so I don't know this. (Anyone have a dead camera?)
I suspect that exposures at speeds substantially beyond Canon's limits are in fact underexposed, and if you had a way to measure depth of field you would find they were taken at smaller apertures.
Here's the thinking:
Exposure begins with the shutter closed. The blades begin moving towards the desired aperture. If the exposure time is long enough, then the blades stop at the desired aperture. When the exposure time ends, the blades begin to close. If the blades move in both directions, the under exposure that happened while the blades were opening is corrected by the 'extra' exposure that happens while the blades are closing.
If the exposure time is too short, the blades never make it to the desired aperture, and start closing. So while it's very cool that the camera will attempt extremely fast shutter speeds (and leaf shutters are inherently fast), I think you'll find substantial underexposure and smaller-than intended apertures at those speeds. Doesn't mean they aren't real, but I think you'll find you need a lot more light than you'd otherwise expect.
Forgive me if you've posted this elsewhere, but which camera do you have?