So... the dealer applied the Firmware update and SatNav now appears to start as normal when ignition is switch on, without 'Checking Navigation Data' error message.
Although, driving with the Sat Nav instructions on yesterday... system suddenly cut out and the 'Checking Navigation Data' error message came on, which never happened before. Solved issue by removing and re-inserting the SD card. If it happens again, dealer will be hearing from me again.
Managed to update the SD Card to latest maps, issue was that I had to slide the white lock switch on side of SD Card to allow formatting of SD Card.
Have to say, updating the maps on this system was a massive ballache. Why do VW have such a shitty Sat Nav system and update mechanism? Can they just strike a deal with TomTom or Garmin, have a professional company deal with future in-car Sat Navs?
With my old, stand alone TomTom unit, would take me 10 mins to update using their download manager. The VW unit literally took hours to download, backup, transfer. Really disappointed, spoils an otherwise excellent car.