It looks to me that the shot #4 is a bit lighter and more contrasty in the overlap areas than #3. Also, I do not notice the rays in #3's overlap area (though it is possible they appeared just as you moved the camera between shots). Increasing contrast in further post-processing probably amplified the effect of the "crepuscular" rays. I am using quotation marks as I am not certain anymore they are really so.
Was there a polarizer used, or any other type of filter, even UV? Lens hood? It is possible that the lighter sky area in #4 is a filter-induced flare.
Yes, it does look a little lighter. The fifth frame, which I didn't use, is lighter still.
No polariser, no; but I keep a Hoya 1A mounted all the time. I had the Canon hood fitted. I rather doubt there was any flare: as my shivering well demonstrated, I (and hence the lens) was in shade the entire time.