IIRC this has something to do with the meta data in the file and the orientation your iPad was in when you recorded the video. If you play the file in quick time i think it will read the meta data correctly and play the video in the correct orientation. you can possibly flip the video using some video players. see the link below on apple forums for reports of the same thing and some work arounds.
https://discussions.apple.com/thread/2482492?start=45&tstart=0
