In what mode are you trying to operate the transmitter? If you are using PPM or PCM1024, the transmitter will ask if you want the "regular" channel order that's historically been used. If you are using PCM-G3, and you change from the older specs, then the transmitter will ask you if you want to change to the channel order used by PCM-G3. You are in full control of the default setups.

If your transmitter is set up one way, then go into the Frequency section of the Linkage menu, change the modulation and then change it back. You'll see the prompt that asks you if you want the channel order changed. Select PCM-G3, and then hit "yes" when the transmitter asks if it's OK to change the channel order to that suitable for PCM-G3.