Here's the movie. My point is that it already looks like the camera is compensating for exposure...which is exactely what I don't want it to do. The sun brigtens, and the camera looks as if it is compensating by closing the iris. This is not what is needed. The sky is not changing that dramatically. What is changing is the way the sensor is responding to the increased brightness of the sun.
Download the file from this link.
Your movie looks exactly the I would expect it to with a camera locked to a fixed aperture, shutter speed and ISO speed. The lighting is changing and the camera is not.
The scene is getting gradually darker as the sun goes down, and the flickering appears to be caused by the traffic, combined with the changes in the reflections in the water.
As I mentioned in my previous post, if you want the camera compensate for the changes in lighting, then you will need to go with a mode like Autoexposure or Aperture Priority (if you want the frames to look close to the same brightness, which it sound like you do).
Given the darkness of the scene with the sun going down, I'd go with Aperture Priority (Av Mode) with a fixed White Balance (as suggested by Freefly)
Personally, Iwould consider using a littlebrighter exposure, too, since the metering is underexposing the scene as a whole with your current settings,because you're shooting into the sun. You can use Exposure Compensation (set to a + EV value)to do this (although be careful not to use too much, or you'll cause blown highlights).
As others have suggested, you can also shoot in RAW, and you'll have more control over the images later. This will also give you more exposure latitude, given the amount of contrast in this type of scene (with both the bright sun and the darker areas in shadows).