Switching the field weakening flag is not enough to get it to work. I strongly advice you to return that option back to its default value to prevent damage to your hardware because keeping it on without proper tuning is highly dangerous.
Pulling the power cord is not necessary to stop the motor. If you are experiencing issues with software, disconnecting the interface cable (USB/UART) is an easier way to stop the motor.
USB is known to misbehave at high power levels especially if the cable is long and unshielded. Try using better/shorter cable, or use UART (it may not be directly accessible with your Komar though).
Did you follow these instructions under section “RCPWM”? Quick start guide for Myxa - #3 by pavel-kirienko