surface difference misbehaving

I have been trying to utilize the Surface Difference command to trim a series of amorphous holes out of a surface and have been having problems with consistency. The setup works fine on at times but not on all surfaces. The script projects a series of closed curves onto a faceted surface and the idea is to trim these holes out of the surface. I works but only on some surfaces.

The intended result looks something like this.

Why won't this work?