(another ksp'er here...)
I think the problem is atmospheric drag, which increases when the sail is open. If you're looking to increase apogee, the most efficient place to do so is at the perigee, which also happens to be where the atmospheric drag is the worst.
So setting the mission, you get to choose the orientation of the sun relative to your orbital ellipse. If the sun direction to the sun is perpendicular to the long axis, then you (presumably) want your sail wide at the perigee, where drag will also be greatest, but will also provide the most efficient raising of the apogee.
OTOH, if the sun's direction is parallel to the long axis, you can try to avoid drag at the perigee, and then rotate into position to get more thrust during the journey from perigee to apogee. But this is a less efficient way to raise the orbit, and will deform (circularize?) the orbit. I might have to fire up KSP with 'cubesat' with an ion thruster to simulate this...