Mayo, thanks for the awesome suggestions! I'm not sure of the exact software version, I will get back to you on that.
We did mess with the turnbuckles and pinions. I didn't think too much about getting the pinions squared up, so that along with the turnbuckles probably being at different tensions might be what is causing the issues.
The CNC does have hard stops installed on both x rails. I'll try on Monday and see if I can square up the pinions, thanks so much for the tips!