That makes it more curious, then. I was Miophysite (horrible luck down there in Ethiopia nowadays) and so was my liege, or at least should have been.No, moral authority is not a factor. Some religions lack the holy war CB (unreformed Pagans, Jains, and technically Buddhists did too) so maybe that was it (11% MA does sound like you might have been Pagan). Alternatively, if you are a vassal you can only use holy war if your religion is from the same religious group as your liege's religion.
Now I'm wondering if the fact my capital got relocated had any effect, if new Jade Dragon CBs perhaps overwrite holy war CB in case you're trying holy war rest of your capital duchy... hardly. And I didn't see new duchy CB either, just border dispute CBs. Duchy in question already had holder, anyway.