PWM control of air core motor
"appears to be a reduced force on the magnet when the magnet is close to being aligned with one of the coils, but no-one has explained why this might be the case"

When the magnet is aligned with one of the coils, the field lines go straight along the length of the magnet and there is no off-magnet-axis component of the field from that magnet to generate sideways force. This is so even though the coil current is at its maximum and is producing its greatest field strength. For any disturbance, the restoring torque will be very low because of this alignment. On top of that, the other magnet will be at the current crossover point and will be generating zero field, so it won't be doing anything to stabilize the magnet position either.

At 45 degrees both magnets are active at 71% of their maximum field strength and the magnet is being held in position by the vector sum of two fairly strong off-magnet-axis fields. If it is perturbed, the restoring force per degree of perturbation is much greater. 

Electrical engineering is not my specialty, but I built my first DC motor out of wood, nails &amp; scrap wire when I was in primary (elementary?) school 60-odd years ago.