Your post doesn't make it clear whether you have coded them or not.
From what you describe it seems as though you need the coding done to remove the error checking on the rear lights. As they are LED's power draw is much lower than normal bulbs. This is in turn is causing your warning gong and its killing the power to these lights as a safety feature, making you think they are not working. Coding should fix that - although if memory serves me right I think you also need the latest FRM3 module, which is your car probably won't have if its of 2007MY.