Thank you for checking Fraser!
Before I eventually rebooted the SBC I got this output (and the motor turning correctly):
| BLDC motor speed can be controlled by setting its Target Velocity (ie its duty cycle).
| The target velocity can be a number from -1.0 to +1.0, where sign indicates direction of rotation.
| For this example, acceleration has been fixed to 1.0Hz, but can be changed in custom code.
Input a desired velocity between -1.0 and 1.0 and press ENTER
Input Q and press ENTER to quit
Strangely there were 4 brushless motor controllers showing up on VINT port 4 in control panel. Two with and two without channel 0. This should have made me suspicious.
After a reboot of the SBC it is now working as expected with the example code and in my application. Also the control panel is only showing one brushless motor controller.
So our guess is that the issue was caused by some addressing issue but we have no clue what could have caused this.
Anyway this is marked as resolved! Thanks!