Kate,
What you are seeing is due to door and window sizing conventions
in the US. A 2'-8"x6'-8" door is the door panel size and the total
height of the outside head frame is usually the panel height
plus the head frame thickness. For windows it is different.
Windows are called out by their outside frame size
so a window set at 6'-8" will have it's out side head frame at 6'-8"
but it's finish head frame under side will be 6'-8" minus
the head frame thickness. AC follows these conventions
so you have to elevate your windows the thickness of the head frame
to have the window finish head and casing line up with
the door finish head and casing.
Peter Devlin