Yes there are obvious differences, I can see your head swivels forwards in the upright one, similar to what I observed at:-
http://prettyill.com/forums/viewthread/712/P30/#4183
Where, at the end, I said it looked like my hind brain (the cerebellum) was being scooped up by the back of my skull and hoiked upwards and forwards towards my brainstem.
Your scans remind me of the results of a study done, I think it was in Aberdeen, anyway I believe it was in Brain Injury 2010, (Freeman and Heffez were some of the authors involved, if you want to search on it) where they looked at the differences in the level of cerebellar tonsilar ectopia (hindbrain escaping through the bottom of the skull) between MRI’s taken laying down and upright. It was quite informative.