Current version is 3-1/63, you should update.
Your current nav version conflicts with your dealer statement "we've checked it with the dealer who said they updated the software and its totally fine."

One of the bigs that will be fixed with the new version:
"The navigation system needs a long time to find the vehicle position"
This is quoted from the BMW Service Bulletin from October 2003, when 3-1/63 as released.

Which sounds like your bug :-)

Get any OS CD from V22 or newer, ensure it is in Mode2/Form1 format, insert it and follow the on-screen instructions.