I have a 2003 330i with a retrofitted MK4 Nav. I did the swap 4 years ago and hadn't had a problem until about 3 weeks ago. I had to have my central locking system relays replaced and so I had my car battery unhooked for a week while I sent it off and waited for it to come back and then ever since I reconnected the battery I haven't been able to get a correct position. When I unhook the battery again or reset/install the firmware it finds my location perfectly but it still doesnt keep that it knows where I am. I also drove 12 hours after I had hooked the battery back up to get home for x-mas break. This is what the settings screen shows:

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