My iphone serial number doesn't match the serial number on the logic board label

Hello,

My name is Nuno and I have an iphone 5 16gb, and after the update to the ios 7.0.3 my camera and volume button stopped working.

Because i have the phone for less than a year, I decided to take it to the store in order to repair the problem or get a new phone. (note that in Portugal we dont have apple stores, but you do have authorized repair shops.)

(the problem stars now):

2 days after I delivered the phone, i received a call from the store saying that was a problem with my warranty. When i get there, the guy informed me that the phone's serial number, doesn't match the one on the logic board.

This said they cannot ask for a new phone, because my phone, quote "might be stollen" or from "black market". I have now to contact apple in order to get some explanation and solution. (Waiting for monday, because theres no call center during weekend)

I bought the phone direct from the apple store web site, I have the warranty and the Phone is 100% legit.

Please let me know if you have the same issue, and if apple gave a solution

thank you