The Dual MC33926 Motor Driver Carrier and the Jrk 21v3 USB Motor Controller with Feedback use different interfaces and require different control schemes. From the rest of your description, it sounds like you are referring to connecting the dual MC33926 carrier. Are you also using a jrk motor controller?
As explained in the “Basic Application Connections” section of the dual MC33926 carrier’s product page, there is more than one way the board can be controlled (e.g. using two input lines, IN1 and IN2, for direction control and one of the disable lines, D1 or D2, for PWM speed control for each channel, or applying the PWM signal directly to the two input pins with both disable pins held inactive). Also, the default state of the EN pin is low, which puts both motor driver ICs in a low-current sleep mode; if you are connecting 5V to VDD like you metnioned, you can use a jumper to connect the EN pin to the neighboring VDD pin to hold it high and allow the board to run. If you try those things and are still having problems, can you post a wiring diagram or pictures showing how you have it connected?