MikMo:
This look to me like you are sendeing something to GoBetwino AND something that is not meant to go to GoBetwino. That will not work.
When you use GoBetwino you can ONLY send well formed GoBetwino commands, otherwise GoBewtino will try to interpret it a commands and fail miserably.
In my experience Gobetwino copes fine with non-command messages, it logs them and carries on just as you'd hope.
However, having the Arduino's serial port held open by another application will definitely stop Gobetwino from working.