Also there is an issue with subsurface scattering in PT with any sort of volume/haze, so maybe it's breaking itself when any volume is applied, because I noticed this without clouds in the sky trying to do an amazon river.
Good example of this is the transparency mask trick with glass shader is completely broken if you apply a fog layer, no matter how faint. It lights up the subsurface scattering, or transparent object, or apparently water.