Moflex based on a quick google search are coded specifically for the 3DS, other formats have to use codecs and those are probably a little harder on the 3DS hardware?
Best analogy I can give is like feeding your cat, one thing is cat food made for cats, the other food is a 300 dollar dinner from some expensive place, your cat can eat both but one will make it puke.
Maybe someone will make a PC converter app (or already has) that can make movies into moflex video's for a 3DS media player?
Edit: I are error... lol