Fixed.
After you sent in a copy of your theme, and we were unable to replicate it with our servers and your theme, we went through all the settings and the whole nine yards.
Turned out, it was your Permalinks for your Post structure. You had it set to “Custom” and /%postname%.html
Adding .html to posts will break your permalinks, and caused the entire issue. Changed it to just /%postname% – resaved your permalinks – and now everything works perfectly.
Ben