Issues building a simple 3-D geometry with COMSOL Kernel

I am building a single foam unit cell, you can see the attached file, and am having an issue where a surface is not being deleted after differencing several geometries. When I use the CAD Import Module Kernel, there is no problem, but we have only one license for it and it is sometimes tied up. Since I am building the geometry natively I don't believe I should have to even use it anyway.

Does anyone have an explanation on why it is doing this, or better yet point out something I am doing wrong.

Thanks,
Mario