Motor timing help

 Hi, I'm trying to get my motors running with LinuxCNC, and I have an old controller for the machine that can move the motors, but the card reader on it is broken. I have tried many times to get it working with LinuxCNC, but now I've tried to diagnose it with an oscilloscope on the old controller. For the x-axis output, the step pin outputs a constant 20MHz signal when not being told to move, but when being told to move, it outputs a 12MHz signal. Image 1 is the motor not moving (Consistent wave), and image 2 is the motor moving (weird-looking wave). I took a video of them side by side and is linked to a google drive. If anyone knows how I can replicate this signal/frequency in LinuxCNC, that would be greatly appreciated. Thanks. Link to video -->  drive.google.com/file/d/1qQ6TFAT_yjkfDdm...Lns/view?usp=sharing
Image 1 -->      Image 2 -->