Hi there
I had recently a discrepancy between the position that the FMS/GPS was indicating and the physical location of the NDB. I could clearly see the beacon but the FMS was indicating another direction. This was due to the fact that some countries have not rechecked the accuracy of the LAT and LONG of their beacons. Such countries are Greece, Iran (in my case), ... There is a very good article in the Professional Pilot Magazine of last month and you would be surprised by the small number of countries who actually checked their references.
Hopes that helps.