The Japanese DVD version of "Rekku no Houmonsha Deokishisu" had a large number of visual edits from the version seen in Japanese theatres and the English version.  Here are screenshots from the two versions so you can see what I'm talking about.  The top images are taken from the original video of the film (which is what was used for the dub), and the bottom images are taken from the edited Japanese DVD.  

I plan to replace the top images with higher-quality images once the American DVD is released.

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The pokemon in this scene have been rearranged.

Since the building Rayquaza is falling against is made of glass, a reflection is added for the Japanese DVD.