Have never used photobracketing. A quick check of the Bracketing readout in the Control Panel shows no correction. And hitting the EC button shows no correction values in any of the shooting modes.
I know that EC doesn't go back to zero when you turn the camera off or when you hit the two Green Reset buttons, so I always check it along with ISO and white balance before I take any images.
Now I have seen this erratic stuff in connection with my SB 800 speedlight. But that was because I didn't really understand CLS lighting or the Speedlight controls. But, hey, I was shooting yesterday in Shutter Priority Mode. What could be more straightforward than that?
I will get an ND filter soon, and I know that I must be careful to use Center or Spot metering so the filter doesn't give any whacko settings to the exposure.