I think what you are hearing is a different sound from the 40D because...
The 40D used an ultrasonic vibration to shake debris off of the sensor and let it collect in an adhesive trough.
The 5D3 uses two tiny highly experienced and fast window washer guys that run out, set up their ladders, open the shutter and clean the hell out of the sensor then reverse everything and get back in their hidy holes lickety split. That's why it takes slightly longer and makes a different noise. The reason it takes longer one time over another is that those guys have to routinely sit and have a really quick beer after they're done or they would eventually start doing a poor job due to poor work conditions.
Don't believe me? Put a clear cap on the body, set up a high speed camera and run the process.