You may have a corrupted tune loaded. Reload the stock tune, start the bike, shut it off, and reload your last tune. I have experienced this problem and found that it can happen if you edit and save a file in TuneECU while you are actively connected to the bike's ECU. So always disconnect the program, then make changes, save the program, re-connect and then download. If the problem still exists, repeat this procedure but try a tune from someone else for use with the pods. There is no mechanical reason that the engine will run differently in one gear versus another. The tune, however, can be quite different from gear to gear.
Hope this helps.