What's the fault code it brings up?

First I've heard of not being able to remap them considering you can buy a bluefin or dreamscience and do it yourself. Afaik there were no changes to the ecu over the production of them.

Where exactly are you taking it? I'd suggest finding a good tuning/performance ford specialist to deal with it, doesn't sound like you're using someone that understands them very well.

We used a Ford satellite dealer to service ours when we first got it, even they didn't have a clue what to do about the fault codes when the eml came on repeatedly.