Telem 2 conflict with offboard control

I’m setting up a pixhawk (genuine 3DR) running Copter 3.3.3 to accept commands from an external Linux computer (Jetson TK1). The two are currently connected via USB on the TK1 to the USB on the pixhawk. For a number of reasons, I want to start using the telem2 port, however there seems to be a conflict.

If I have the FTDI cable connected when I power the pixhawk the main LED goes solid red after a few seconds, but I can connect to the pixhawk with no warnings or errors. Alternatively, if I plug in the FTDI cable after the pixhawk is all powered up, it stays happy (no red LED), but I can’t connect to it through telem2.

According to the documentation I could find, the only settings that appear to need changing are the Serial 2 Protocol (set to 1 for Mavlink), Serial 2 baudrate (set to 115), and serial 2 RTSCTS (set to auto). I am using this FTDI cable and wired according to here (hardware setup at the bottom–it’s a PX4 page, but the cable wiring seems to be correct and what I want).

Is there another setting? I’ve tried searching to see if there is something else that uses serial port 2, but haven’t turned up anything. Any other ideas on how to troubleshoot this?