It seems that religious unrest can be caused by characters of other religious in the area, even if your province is 100% your religion. It might also be that some regions are hard-wired to produce heresy, and heresy comes from within and of course causes unrest. So maybe a build-up of unexplained unrest is the prelude to the appearance of a heretic or at least the outbreak of measurable heresy on the relgion-o-meter. But I don't know.