I think it's the way you are working. It seems that you do one view that isn't 100%, and then you try to fix it in another view when you should be fixing it in the first view. If you have the SCH just duplicate it exactly in the SCH view and make sure it's right, ie no red ends, grab junctions and move them and make sure all the wires go with it, etc - your C1 isn't connected to VCC -. If you have the SCH view you don't need the BB view so don't even bother laying it out.
I bet if you opened a new window and copied every thing in the SCH view and got it right, I bet it will be right in the other views. There is something in FZ that it's best not to do something in one view and fix it in another view.
I guy did this board with maybe 100 components and it was fine.
