I've tried reinstalling, and with and without the patch, but there's no difference. Now, although I've not played much of Forged Alliance, I got the impression that it was very similar to the original, only with more units and a new Heads Up Display - nothing to cause such a massive drop in performance. The particular setting that has the most impact is called 'Fidelity.' Most other settings (even the addition of 16x Anti-Aliasing) have very little effect on the framerate.
During a typical scenario (a base with some units) I get nothing more than 6-7 FPS on anything more than Low Settings. People then started to play Forged Alliance, so I installed it, patched it and started a game: awful. We started with the original, and I was pleasantly surprised with how well my notebook could play it - around 18-20 FPS with all Settings on High other than Anti-Aliasing, at 1440x900. Recently, along with several other people I know, I bought the Gold Edition of Supreme Commander, which contains both the original, and the stand-alone expansion, Forged Alliance.