It sounds like you might be measuring the current input to the driver board with your multimeter and assuming that should be the same as your current in the SMC software (which is the current through the coil of the motor). That is not necessarily the case with a motor control system that uses switching frequencies several thousands of times faster than the measurement rate of a multimeter, capacitors on the board that buffer energy, and an inductive load like a motor coil that buffers energy and resists changes in current (even when the FETS on the motor controller disconnect the coil from the power source). It is a little unexpected that the current from the power supply would be 500mA higher than the current through the motor coils. Can you post pictures here that show how you have everything connected for that measurement?
Also, it is not clear to me how that is preventing you from implementing some sort of stall detection. Generally, the full stall current (when not being artificially limited by a device like the SMC) of a brushed DC motor is several times the rated continuous current. When I spoke to you on the phone yesterday, you said you set a current limit for the motor of 1.0A. Does the current (on the status tab of the SMC software) ever drop much below 1A (like when the motor is free spinning)? Can you post a datasheet or any specifications for the motor you are using? What kind of power supply are you using?