Hm, when running Challenges automatic, it only works if the browser tab/window is in focus, otherwise it will not run. I use Chrome, does this happen in other browsers also?
For all those that haven't noticed yet, When you get a mastery lvl, you get a boost on Production, 0.025, 0.025, 0.05, 0.05 and 0.1 respectively to the lvl of mastery (if I remember correctly). When you ReForge, you get to keep those Production boosts, but you start again and you can obtain those masteries again. That's how reforge works, start again and keep the production, not get more production only by reforging.
Do you have a kongregate user and adblock disabled?