Getting help may be a problem. That controller was developed and built specifically for DYNACNC and in the process there were some issues between DYNACNC and the vendor. The relationship ended on less than cordial terms. Since DYNACNC is dead and gone and along with it any technical knowledge of their proprietary controller, and the vendor has been less than helpful, about all I can do is offer you general suggestions:
replace the encoder wire/cable (if it a differential driver cable you may need a new one). They came (at one time) from US Digital.
Open and carefully clean with alcohol the encoder wheel.
If it continues replace the entire encoder
If none of that works then consider replacing the X axis driver.
If THAT fails then grab your ankles ( the nest solution is painful)
Both problems appear to be encoder related.