So... I ran into this problem with subdirs..
I have everything running on Git with no errors but on Localhost for some reason some of secondary subfolders were not showing their index pages just their own pages..
All displayed correctly.
where I have the categories loop included..
Would not show on localhost.. yet fine on GitHub..
After scratching my head for hours and no luck with google.. I tried all sorts a stuff and then had a random stab at adding /index to my permalink.. and well hey presto!
If that's of some use to you then kool.. If not "Move along - nothing to see here.."