Okay started digging into it this morning. I feel like I have everything set the same as what you had but it's still not working correctly. The attached plan is the actual plan that I am currently working on. I have all three walls in and windows set, I know its not perfectly centered but I am more concerned with figuring out why I can't get it to work properly. Please take a look at it and see what might be the problem.
This is blowing my mind!
CChance_Dormer.plan