The message "Waiting on NAK" is correct. This is just a waiting message. This message is displayed when the SW Flow Control setting is set to Xmodem.
If the CNC is not setup to also use Xmodem or the CNC has not started the RS232 read/write then the Calmotion will display this message as it waits for the CNC.
The CNC must support Xmodem. If CNC does not support Xmodem, then this SW Flow Control setting can not be used on the Calmotion.