Hello Neoh,
Are you using BMW Navigation Mk 3? or Mk 4? Mk 3 uses CD ROM, Mk 4 uses DVD ROM.
If your car is a Japanese import, the navigation system cannot function locally without some modifications. The Navigation computer that came with it is not compatible.
But if your E39 is from UK, you are in business. I have the version 07/08, for Malaysia and Singapore that I'm using in my E85 (which is similar to the E39 and E46).