I've been getting the 'Checking Navigation Data' problem on the Discover Media system in my 6 month old Golf SE Nav. Have a dealer visit booked in a few weeks time.
Would it have anything to do with the current maps in the car being out of date?
How often do VW release updates for the Sat Nav?
The issue is typically with the head unit in the glovebox, not the SD card itself. The dealer will apply a firmware update which typically solves the problem.