For the toolpath issues, check the machine mechanically — belt tension, pulley set screws, and if you are cutting a slot just as narrow as the endmill add geometry and cut as a pocket down to tab depth or the penultimate pass — where possible avoid slotting and add geometry and cut as a pocket (Making vacuum hose adapters and/or Adding geometry to cut as a pocket with a finishing pass ) and consider leaving a roughing clearance and taking a finishing pass.
For the loss of connection, that is most likely EMI — contact us at support@carbide3d.com and we’ll do our best to sort that out with you.