dbradf How do I test for an orthogonality problem?
Good enough to check by using auto-guiding :-).
Go do a guide calibration near the celestial equator, and say, within an hour of the Meridian (to reduce atmospheric refraction problem). Check the red and blue vectors in the small calibration window when done. If the red and blue lines are 90º from one another, you should be good to go.
Notice that when you throw that "Flip" toggle switch, the PHD2 simply reverses the blue (right ascension) vector. If not 90º, an acute angle becomes an obtuse angle after flipping. That is what you don't want. You want the angle to be 90º for both flipped and non-flipped.
Incidentally, when you calibrate close to the pole, the vectors will not be at right angles. PHD2 will make the appropriate correction if you calibrate at equator but guide near the pole. If you calibrate near the pole, and then autoguide near the equator, PHD2 still makes a correction, but the error is much larger in that direction. This is why you want to calibrate near the equator, or at least within 30 degrees of it.
Chen