I have a similar problem. I believe it is somehow related to the SODE gates though. Every time I use the SODE gate on startup, the performace becomes horrendous immediately - e.g. all animations of GSX objects lag. Interestingly, this does not in fact affect FPS directly - instead the game starts to pause for a while, I have issues with the sound, textures load slowly. It continues throughout the whole flight, even when they are certainly no GSX objects/gates within sight.
Best, Jan