Checkboxes not respecting Category rules

I’m using the Checkout Custom Fields module with two checkboxes. I’ve specified that they should only appear on 1 or 2 categories, but they are both showing up for all categories *in the order confirmation emails* both to the buyer and admin.
I’ve also tried specifying every other category as Excluded, but that didn’t change the result.
Do I need to set some option differently for this to work properly?