Stepper motor noises change at random
Because "5000" steps one way and then "5000" the other doesn't result in the original position, it's indisputable that you're missing steps.  A could of ideas to narrow it down:


Try without micro-stepping.  Repeat the 5000 step exercise with full steps.
Change the speed. You might be right on the edge of a resonant speed, which can cause the change in pitch you describe.  
And yes, definitely use a trapezoidal speed profile as another suggested already.  Going from stopped to 1428 steps/sec is an abrupt start for sure.