Steppers don't work as expected while printing
I've looked into your configuration file of your firmware but cannot find anything that describes this odd behavior. You have used some conservative settings regarding printing acceleration. What cannot be assessed is the amount of steps required per millimeter movement of every axis, that is left for you to re-check.

Note that when the steppers are working as expected when the printer is at idle and you command the printer with an external printer software (e.g. Pronterface from the PrintRun software suite, Repetier-Host, OctoPrint, etc.), the problem could well be caused by the slicer and/or the options used for slicing the print part.