Unfortunately I just had to declare this thread unsolved again, because the solution GraphicGeek suggested only works for 720p videos. iTunes does NOT allow me to import 1080p .mov files.
To get the 1080p mov files on my iPad I use the SD adaptor in the camera connection kit.
I just make the following folders:
DCIM/100DICAM
Then copy all the jpgs, raw, or mov files to that directory.
You have to have the files named in digital camera format,
like IMG_0001.jpg , IMG_0002.mov, IMG_0003.CR2 etc
but they all import fine.
If they have different names,
I use bulk rename utility to change them on the card.
Canon 5D II 1080P mov files import directly and can be edited in iMovie too.
I've used Clipwrap to convert Canon AVCHD MTS files to MOV.
They playback fine but some 1080i ones have issues being edited in iMovie.
Hope that helps, works great here with my files.
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