Runway not where the gps points

I have added several downloaded airports and until I decided to get to know ILS/GPS landings had no problem as the IFR/GPS combination put me more or less in the right place.

This is sometimes not the case when I do an ILS/GPS approach and find, at the last minute (in poor weather condition) that the white line "Nav" approach is not in line with the selected runway, sometimes by quite a long way too. Is this because my downloaded version of a particular airport has overlaid the Microsoft Sim version and shifted the runway?

I landed into San Juan, Puerto Rico yesterday and found that not only did this runway outness happen but there was a shift in the terminal area too, with grass where there ought to have been tarmac and airplane tails were sticking out of the terminal building itself!