Hi @hyeflyer,
You can try grounding your Shapeoko, which helps minimize or eliminate EMI related issues. Even before that, grounding your dust collection setup would be the very first step as this is a common cause. If you still have trouble, feel free to contact support@carbide3d.com and they’ll have recommendations for you on this issue.
There is probably no link between your using the BitSetter/BitZero and the occurrence of those problems, but sometimes EMI gremlins thrive on subtle changes in electrical/grounding arrangement