Saving the guide settings saves to the device associated with the current Activity. It can be a bit confusing and is simpler in 1.5. Meanwhile, just make sure that you first open the Activity which has the target channel device set in the ‘Opens Remote’ field. Then setup the guide for that device and Save.
The guide that is displayed during the time when no Activity is open or Roomie has just been launched fresh is for the first channel changing capable device in your device list.