I don't understand how you can load a quilt the wrong way. I sometimes load a quilt with the top and bottom to the sides if I am doing custom and want a larger area to work on before each advance.
If you have fullness in areas, you can sometimes shrink it with some starch or best press, then iron it.
The behavior of the LAer is really strange, and no, you shouldn't have to pay for a partially completed top.