You didn't say words to this effect: "all the layers in the problem comp are 3D".
Mixing 2D and 3D layers is a sure-fire way to mess things up.
Layer styles and adjutsment layers can break 3D rendering. Look into that. Also check your OpenGL settings.
Thank you for the insight guys. I've sucessfully used 2D and 3D layers together in the past without issues. Of course every project is different and I might have the perfect combination of layers etc... that is making it all out of way. Still, it's counter intuitive that this wouldn't work. The 2D layers should be completely ignored (just background textures), and these particular 3D layers are right next to eachother at the top of my composition. Would have expected it to work. In the meantime I'll trying one of your suggested work arounds.