"Factory reset" resets all custom settings to ensure there will be no conflicting settings due to user failure, unfortunately it is necessary to reconfigure what has been customized, but it is the most functional method for many problems: unfortunately it is faster/easier reconfigure than find out exactly what is conflicting.
Well, I feel a little silly, but I figured it out. The issue persists with my xbox controller, but I figured out why the ps3 controller wasn't wanting to work. I had the p1 controller set to default like the rest of them, which defaulted to the xbox controller which only worked when I replugged it in.
When I set p1 controller to the ps3 and p2 to the xbox, things are working well enough. The ps3 controller works in games, but the xbox controller still needs to be replugged (I may not use it much from now on anyway)