Tried as suggested using more spies:

Used 10 spies from various settlements and quickly gave traits/ancillaries to make them subterfuge 10. Put them in Antioch (one of my 15% unrest settlements, as good as any other, but since I got half the world it seemed far away enough to elminate any variance) and ended turn 5 times. No spy detected and unrest stays. So I suppose that kind of proves my point that this unrest is some kind of bug.

Similarly, my capital (when pure or nearly pure with my religion) always gets 10% religious unrest if it has a governor.