My Sync 3 system sometimes shows “Navigation Malfunction”. The problem is not permanent, meaning is appears and goes away after I turn the car off and on several times. I suspect the aftermarket GPS antenna to be the culprit, not sure though. My car is Ford Fusion 2013. I converted from sync 2 to 3 and everything goes like a charm except for this sporadic error message.
I am currently in Jordan, Middle East. My car was imported from the USA with a non-Nav APIM. I bought an EU APIM with 64GB and did the conversion perfectly. I adjusted the region settings using Forscan all seems good so far, except for the problem I cited above.