It's possible that the iPad GPU doesn't support all the operations Handbrake encodes and has to have the CPU decode them (resulting in higher CPU and increased

It's possible that the iPad GPU doesn't support all the operations Handbrake encodes and has to have the CPU decode them (resulting in higher CPU and increased power usage), whereas the media in the iTunes Store might have been encoded with only the operations supported by the GPU. This is just a theory, however it's certainly plausible.