Advise needed how to create a 768x1024 (portrait!) H.264 MOV for iPad

[pixelpartner]

I have made some rather uncommon mp4 files that play fine on VLC, but won't import to the iPad/PhotoApp.
When I use VLC convert mode to change the container to MOV (accepted by the iPad's Camera Connection Kit importer), the video gets jerky (back/forth unpredicatable).
Other MOV files created in this XGA potrait resolution with a QT7 compatible EXE, work fine.
The reason, I choose this uncommon format: It contains right over left view with black borders - compatible to some openKMQ 3-D viewers. http://openKMQ.blogspot.com
I hope someone with much more experience can give advise or give it a try.

[pixelpartner]

Meanwhile, I found out that the max Datarate for H.264 files on iPad is 1.8Mbps, regardless of player app.

[Case]

Does that mean your portrait oriented movie wouldn't import only because of the high data rate?