Trimming openings on ondulating facade

Hi all,

I am having an issue trimming openings on an undulating façade I am working on. 

I worked on a 2D plane to create the pattern and then flowed it along the surface in grasshopper.  Up to this point there are no problems.  But when I try to trim the openings on the surface (either by using the trim Rhino command, by extruding the curve as normal to surface in Rhino, or trimming surface and curves in Grasshopper) I simply cant get it to create the openings. As you can see I can trim the top area, as well as openings on the sides, but I cant open the ones in the middle. 

I've been working on this all day and I was wondering if someone could give me a hand or idea as to why this is not working. 

Thanks a lot!!

David