Hi Blake,
I am not on my computer as I am visiting the Maxon Summit this week. So I have to do what I think is not the best way to do it—guessing. Sorry about that.
Having a whole scene (or a larger group) in a Boole might not work when one part is not ready for this.
Take the most complete object and test if a cube can Boole it. Perhaps with the group either under a Connect Object or Booled first, or even merge all first. Those three might hold one option to explore further.
Please note that Multi Instance might be source of trouble here, if the Cloner is set to this.
My best wishes