I would now recommend doing a Reset of the nav.
press and hold <, > and i (or the button next to eject) for about 30 secs (or until you see the VW splash screen)
Then turn off and remove the MFD3 completely from the car. Wait about 2 mins and then reconnect the whole thing. Sometimes they just need a kick up the hoop.
I had to do that process when i had a similar problem as you describe. Touch wood it's been fine since. You don't normally have to remove it to reset but i tried the reset about 3 times previously and it never worked. I was then told about removing and that cured it.
Otherwise i suggest getting someone with VCDS to take a look and ensure it's coded correctly.
The only reason i can think now of it not working is the GPS Almanac (basically a list of where the satellites are in the sky) is not keeping it's update. Usually what happens is you update the firmware and the Almanac gets erased. It can then take up to 15 mins for it to rebuild. But once it has it "Should" keep it and just update what it needs.
Where abouts are you in UK. It might be worth looking at the VCDS register and PM'ing someone nearby.
You can also use the other firmware i linked. It just takes slightly longer to sort out Regensburg but still way quicker than what you experience.