Do you have a lot of current in your tank? I have read that bettas do not like high currents or surface agitation. When I clean do water changes in my betta's tank, I turn his filter on high to quickly snatch up any particulates. When I do that, he hides inside his skull where there is no current to be had. He really hates current. I have his filter baffled with some filter media so that the waterfall doesn't create a surface current. That could be an issue as to why your fish is hiding. My fish takes refuge from it any time he can. Just a theory.