iPad Why can't I transfer these movies?

Hey there.
I was transferring some movies to my iPad 3 as I'm taking a long flight at the end of the week and want something to watch in my iPad.

I have all my blurays ripped to my computer so I can stream them to my Apple TV 3 and watch them without having to get the bluray.

Anyways, my point being, I found some movies which I just can't transfer to the iPad. iTunes tells me it's not compatible.

This is one of them. Any idea what is causing the incompatibility? (As I said they're played fine in the Apple TV)

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Another one:

 

I guess you're talking Handbrake presets? In my case these didn't come from Handbrake.

What I do is rip the movie to MKV with MakeMKV and then put it into a M4V container using Subler. (Much more faster than handbrake as it throughputs the video).

That's why I don't really understand it. Why some movies will transfer and some other just won't.