Yesterday and today I have not been getting rep from doing any patrol missions. And I did quite a few without realizing it. Quick rundown of my steps after bug: I had a exotic weapons mission that auto-completed. (Awesome, by the way ;) ) I got my faction mission from Future War Cult. I had 8 bounties completed and ready to turn in. So I went from 32 to 34 immediately. Ran around with looking at new content / dissembling my emblems and shaders, etc. for room. Did all the PvE missions for the day.