damn.... old, old thread. sorry...
or use a better video player on your ipad.
I use Oplayer, good and plays divx, mkv etc etc. There's a free ad supported version you can use to try it out.
This way you won't be reencoding already encoded video...
Worth bearing in mind there's a issue with some audio patents on the ipad ( presumably because the patent owners know Apple is where the users are prepared to pay for decent apps) so no current ipad video app can play dts or ac3 audio tracks within the video file... I've been using a free Mac app called Adapter to delal,with it - it reencodes the audio only, passing thru the video - so no loss in video quality and of course much quicker.
Oplayer works great with the Seagate Wireless plus external had drive too - just use the built in 'web browser' to go to 192.168.0.1 and use Seagate web app to transfer or stream any codec to your ipad.
