Thanks for the screenshots. I suspect that black doesn't properly clip every cloud, maybe just 99.9% of them. It doesn't catch all of them because of the extreme values generated by the clouds in some places, and due to the way the mask feature is implemented in the Easy Cloud.
Try unchecking "Clip near colour". Normally I'd say to uncheck clipping on the far colour, but in your case it's the opposite because you swapped the near and far distances. You don't need to swap the distances, you can swap the colours instead, i.e. make the far colour black and the near colour white.
Turning off the clipping allows the black colour to continue into negative values beyond the distance where the black occurs, and this should remove even the most persistent clouds in the distance.