Did you do a new full install of RadarBox 2009, or did you do an upgrade.
It you did a full install, then you might want to copy your main database file from the old installation to the new one. This is named NavData.db3
In answer to your question, the auto-populate function works whenever you are connected to the Internet. If the Flybe aircraft were in your old database, then these would have been auto-populated. The new database hasn't auto-populated yet, but it should do as you pick the aircraft up.
If auto-populate isn't working, have you granted permission for RB to access the AirNav server through your firewall. As this is a "new" program as far as your PC is concerned, permission is needed.