I'm not sure what you mean. There are two lights on top of the 3GX. One is a status light, and one is a Gov light. On the status light, green means heading hold mode for the gyro, and red means rate mode for the gyro. On the Gov light, red means the gov is off, green means the gov is on. If you are using a 6ch Tx, then your gov light will always be red. Hope this helps.
When you did your DIR setup, did you set the throttle gov positions? I guess the first question should be what version you are running. Also, are you running satellites only or a separate Rx? If I remember correctly, the XG11 is a DMSS system, and the 3GX is not compatible with that system with just satellites. But, I need to check with you since I htink you cna get that Tx put back to DSMX.
You will need your Tx on, then plug the helicopter in so that the 3GX is on and initialized, you should have a green light. As for the actually flashing, the video below will explain it better than text. It's for 3.0, but it works the same for all versions.
Rc-Help - 3GX Setup Part 2 How To Flash The Firmware To Version 3.0