Hi, Ronin26
Sounds to me your step's Per are set to an Inch Value, Mach work's in unit's , thay can be eather MM or INCH.
Go to Config tab select Motor Tuning and Setup, change the Step's Per to a value that gives you 1 MM of travel, don't forget to click on Save Settings button for each Axis.
You will probably need to re-tune Velocity and Acceleration also.
Hope this Helps, Chip