Leadership value and all that should be applied after you press the start button. As for how long it should take and how many NPCs to use and all that jazz, it's in character info so find a production group and see if they'll share any tips.
The estimated value just uses stock values to predict it. Depending on what you use, you could be consistently under that predicted value, or as in your case over it. I suspect, as mentioned on IRC, that you have too few NPCs working.