I can see how this is confusing, although intended behavior.
Maybe something can be added to the standard notification explaining for what position the protests are.
Perhaps title change? Like this:
Knights Protesting the Judge! (just in)
Protests against Katrina Dragul, Grand Duchess, High Justice of Morek Empire, Royal of Morek Empire, Ambassador of Morek Empire, Duchess of Volkvangr, Priestess of Sanguis Astroism are increasing, and result in a loss of a point of prestige for her.
Knights Protesting the Ruler! (just in)
Protests against Katrina Dragul, Grand Duchess, High Justice of Morek Empire, Royal of Morek Empire, Ambassador of Morek Empire, Duchess of Volkvangr, Priestess of Sanguis Astroism are increasing, and result in a loss of a point of prestige for her.