Trim Solid producing Invalid Breps

Hi, 

I'm trying to use a bunch of small extrusions to subtract holes from larger ones. I've been using 'trim solid' in grasshopper.

Sometimes it identified the cutter geometries as closed breps, so i added a cull component to exclude open ones. Now it doesn't give me errors, but sometimes the trim output has "invalid breps" and doesn't bake.

Can anyone explain why, or suggest a better solution? I'm uploading a part of the full file. In the big one there are dozens of these shapes to trim, so the faster the better. 

The layers in the .3dm should be pretty easy to figure out. 

Thanks!