Hey Lars,
Yes Windows. I'm on a render machine that we custom built to create renders and shows on.
We are doing large prints to ARCH C and D sized PDF's.... but here's a little thing.....
I realized that the chunks were all rectangular. So I went through a selected the affected windows and hit "Bring to front". That seems to fix the issues. It's as if there is a some sort of ghost view/window/object that appears overlapping the lower layers. I can't see it until it shows up in prints. But if I highlight all the other objects and "bring to front" the ghost is relinquished to the back.
As long as I do that it has no print issues.