@Jman841 @shaun @schuermannsebastian
Ok, we have found the cause. According to APM wiki:
then you can force bootloader mode by shorting the CTS and GROUND pins on the radio while powering on. The red LED will light up when in bootloader mode.
This applies to all 3dr radio derived design as well, including the FRD900.
By default RPi GPIO on boot is low, which results in the problem that you are experiencing. We will try to add a software workaround, but for now the best solution is to not connect CTS line.