I have exactly the same problem at the moment. The only way i have resolved it in the past, is to take my car to my local dealer, where the keys are re programmed. It's a fairly straight forward procedure which takes about 2 mins per key, (remeber to take all your keys with you) If that fails,the on board memory has to be cleared of all previous codes,in the workshop. Had it done three times so far in 2.6 years. it's annoying,but a new control box outside of warranty is a killer.
Hope this helps