Yes, I use custom queries via WP_Query and the only difference in either category is the number of posts called. But I’ve tried to interchange the number between the 2 categories and the category/news/ still works while the category/features/ doesn’t.
I also don’t find any settings on wp-pagenavi that refers to number of posts per page. I’ve also tried to use the updated code found in Scribu’s post and the problem still persists.