It happens with scatterer for me too, I actually had that loaded when I first noticed this. Thanks for the quick reply tho, I will try the first suggestion and report back.
EDIT: EnableAtmosphereExtinction only worked in one specific setup I tried: with Scatterer, EVE, and PoodsOPMVO installed for OPM, and without GU installed. Once I installed GU, the problem came back to the OPM planets, which I find a bit odd.
In the one case it did work, it was only for planets with atmospheres, which makes sense. And moons like Eeloo still weren't eclipsing right, so I wasn't able to fix that in any case. I was doubtful that it would be the modpacks like you suggested, but I am curious what GU was doing to mess with OPM.