I am having the same issues with a serial radio. Need to change the baud rate. I configured serial 2 as telem2 port / sys_companion and changed the baud rate and this solved the problem.
When I use the extras.txt it seems to screw with the sys_companion
I also need to to this for telem1, but don't want to hardcode this as I want to be able to swap radio's if necessary and change baud rate in the settings through the GCS preferably. Any ideas on this?
On Ardupilot this is way more easy to configure per serial port.