Ok, I think I have figured it out. It has to due with part numbers from the tanks. Not sure why it would choose to drain fuel unevenly like that though. Shouldn't it just draw from one fully, then the next?
It's strange, I cannot replicate this with a simpler design. The engines are furthest from the forward tank, but for some reason it draws from the rear tank more
Today I created a space plane with an open center section using the awesome B9 mod (I used basically trusses that left an open middle separating the front section from the back on the sides of the plane). As I was flying I noticed my fuel tanks were drawing unevenly (I had one fore and one aft). We know that the program preferentially draws from the tank furthest from the center of mass. This means as long as you don't have a fuel tank directly on the center of mass the program will automatically maintain the starting center of mass. Perhaps I'm over excited but my initial testing seems to show this should be the case.