You're right, this is a failing of the FDE concerned. You can adjust the CofG to the right place in the aircraft.cfg (well, you can in FS9, I haven't actually tried it in FSX) by adjusting the wing_pos_apex_lon = value in the [airplane geometry] section of the aircraft.cfg; increase the positive figure to move the CofG backwards.
This is by no means an ideal fix as many here will tell you, since it affects other FD parameters. It does however get the CofG to the right place and stops the 'shuttlecocking' effect of the CofG being in the nose, without having to re-write the whole FDE. The knock on effects it has are largely unnoticeable IMHO.
