[Topher Welsh]"To me, if you have it set on Manual there shouldn't be any kind of shifting like that. "
I just checked my own GL2, which is always set to full manual and I didn't see any light shifting. The gain didn't change, nor did the F stop or shutter speed, all of which will definitely affect the light coming in to the camera. Perhaps you could try replacing the memory battery, but that really does is to remember your last settings as well as the clock time/date, etc.
The other thing you could try is to toggle the electronic ND filter button on and off several times just to make sure that's working properly. The light shift from turning the ND filter on and off is pretty substantial though, so you'd know right away if it's the same amount of shift as your recorded video.
Other than that I'd suggest taking the camera to a qualified Canon repair facility.