Hi @chris
this is a question for someone on the brep intersection team.
I’ve created RH-67429, where you can follow progress.
To help the team, would you be able to send the original non-intersection geometry and the intersection call you use, without other components or installation overhead? (This would be a reproducible case). I’ll then assign it to someone on the team. There is already enough food on my plate with mesh intersections 
Thank you!
Giulio
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Giulio Piacentino
for Robert McNeel & Associates
giulio@mcneel.com