Arduino Due randomly resets to Programming Mode


I'm using Arduino Due for a project, connected to a computer with native USB port.
I used cmdMessenger to communicate with the PC monitoring software.
the problem i am facing is Arduino Due resets to pragramming mode randomly and stops running the software. pressing the reset button on arduino does not seem to fix the problem, i have to reset many times to get the due working or upload my sketch with Arduino IDE again to get the board working...

an anyone help?

BTW. i'm connected with 9600 baud rate so its not 1200 that resets the due.

Thank you in advance :wink: