I pulled out my n800 and can't duplicate it. Try deleting the GPS from the bluetooth device list (and/or remove any entry that matches the BT address from anything in /var/lib/bluetooth/), then redo the pairing. Also don't open an xterm, just reboot the device (after re-pairing the GPS), and start it in a place where the sky will allow a lock and see if the indicator turns yellow or green.

I'll look into it further, but it is a very subtle problem.