Code:
## Some sites/authors/stories (notably AO3/OTW) add empty p tags where
## they aren't intended by the author during document upload and not
## all authors know how/take the time to fix it. This feature removes
## all "empty" <p> tags, ie, those containing only whitespace or <br>
## tags. Literally: <p[^>]*>\s*(<br/>)*\s*</p>
#remove_empty_p: false
So apparently I need to change that to
<p[^>]*>\s*(<br/?>)*\s*</p>
Gee, it sure would be nice if I knew a story that was exhibiting the problem to test with... 
-- My bad--I missed seeing the URL.