Check the auto normals settings in E3D and also check the Boolean settings in C4D. turning off "high quality" can do miracles sometimes. Likewise, dropping the boolean in a connect object or applying a reduction deformer can work wonders....
Thanks for your reply Mylenium.
I tried turning off high quality but that actually made it a bit worse. I don't have access to connect object or the reduction deformer since I am using C4D lite. Gosh darned C4D Lite users eh.
I would just resort to doing 100% spline modelling since that doesn't give me issues. It's only when I use booles. But having the gap look like that, where the face is flush with the face of the other line I can't see achieving with just splines.
Well, once again Element3D proves to be an amazing plugin! I just turned on "auto normals" in Element3D and it fixed it all up nicely.
For anyone reading this with the same issue, and you don't have Element3D, I recommend buying it (videocopilot.com). It is defiantly worth it and makes C4D-AE integration very quick and smooth (to put it briefly).