This question has been asked before: What happened to my Mach3 Motor Tune-up in the Configure tab, it has disappeared but had been there before. The previous answers were to go to config: motor tuni

Motor tuning is the third option down when you click the config menu option. I have never used the motor tuning dialog from anywhere else. If you are looking for the button to calibrate the axes, then go to the settings tab and click on the button that says "Set Steps per Unit".