Could be a bit of, er, grit on the starter motor spindle.
Have a look, clean it, but do not put anything more that a trace of thin oil on the spindle otherwise dirt will stick to it.
PS Read your post fully,it must be the starter motor not aligning correctly or fully.
There is a lot of torque generated by a starter motor so it must be correctly and firmly fitted,but do not overtighten the securing bolts and risk stripping the threads.Jerry