The main problems are, that video is not really part of the epub specs and the iBooks app on the iPad is a crap program. The iBooks program doesn't follow a lot of specs and you have to work around it.
Then again, after working around it, it will probably only work on the iBooks app.
Like I said, video is not part of the specs. If you get it to work, there are no garantues. I would advise search around on this forum. Various posts about video on the iPad in a iPub (since it won't be an ePub) are made and I believe also methods to make it work.
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