I have noticed the same issue with the step pulse value, if you enter the value you want , choose save setting and then close the motor tuning dialouge box it will save your setting but each time you open the motor tuning dialouge box that value will drop by one . I have it set at 11 and each time I open motor tuning it drops by one to 10 , 9 , 8 and so on , you just need to make sure you type in the value you want and click save axis setting every time you open motor tuning.