If you bake the elements that you are trying to Boolean, and then try to do the Boolean in Rhino, does it work? If it doesn’t, the problem then is the core Rhino geometry engine. We find many situations in breps where definitions stop working because of this limitation. Mostly fillets and booleans, sometimes even trims.
You can see if you can move the difficult areas away from the intersections of the different breps. I know this si not a good solution if you have to change the design to make it work with the current way Booleans work, but it might be an acceptable workaround sometimes.