Most of the video converters out there, other than Apple or Adobe products do not recognize orientatio EXIF meta data. For example, my video files, taken in landscape mode with the Home Button to the left, are upside down with VLC.
Here are links to four short MOV files showing the four orientations for the iPhone 4S. I had to upload them to DropBox for you as all of my available Cloud based mail programs choked on saving or sending these little video files.
http://dl.dropbox.com/u/7584570/IMG_0061.MOV
http://dl.dropbox.com/u/7584570/IMG_0062.MOV
http://dl.dropbox.com/u/7584570/IMG_0063.MOV
http://dl.dropbox.com/u/7584570/IMG_0064.MOV
I usually record hockey games in Landscape mode with the Home Button of the iPhone on the left side with the screen facing me. That is the mov file IMG_0063.MOV
Apple's QuickTime Player displays it correctly, while the VLC player, which ignores exif flags plays it upside down. So does the Plex Media streamer ignore the flag, so does the thunderbird mail app ignore the flag, and so on. Adobe looks at the exif flags so they get it right.
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My movies are of four Post It Notes, each one describing the location of the Home Button. Take a series of four pictures oriented like my test MOV files , then take 4 short MOV files of the same iPhone orientation. If the results are "misoriented" then the software you are using to look at them is ignoring the orientation flages.
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For more detail of this subject look at*
ImpulseAdventure - JPEG / Exif Orientation and Rotation
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JPEG Rotation and EXIF Orientation
Digital Cameras with orientation sensors allow auto-rotation of portrait images. Unfortunately, support for this feature is not widespread or consistently applied.
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Digital Cameras with Orientation Sensors
Many newer digital cameras (both dSLR and Point & Shoot digicams) have a built-in orientation sensor. Virtually all Canon and Nikon digital cameras have an orientation sensor. The output of this sensor is used to set the EXIF orientation flag in the image file's metatdata to reflect the positioning of the camera with respect to the ground. Canon calls their sensor the "Intelligent Orientation" sensor. It is presumably a 2-axis tilt sensor, allowing 4 possible orientations to be detected (shown in the left side of the diagram in the link above).
