Maybe if you lower the quality of your ship effects you will see an increase in FPS. That would make the jump effects less pretty to look at though...

Its a known issue. There is a similar FPS drop (though not as severe) in Trinity during fleet phase jump startups.

Lowering the quality of ship effects has NO effect on a TGA texture. TGA textures have no Mip Mapping capability. Most of the particle effects use TGA format. Even on lowest settings a TGA texture remains the same resolution. Which is why we replaced all of the TGA textures with DDS in TSOP. This was because of DDS formats mip mapping ability, and it worked on the particles.

No worry's, You don't know unless you ask right?

The only details that get changed when you set high, medium, low in the options are the ship, structure, and planet textures, because they use DDS format. Some of the particles use DDS as well, but very few of them, and they get changed with the settings too. However, the ones that use TGA format remain at max resolution no matter what the settings you use. I tried to talk IC into using pure DDS format just for this issue, but they insisted TGA was a better format. Which it is from a detail perspective. A TGA texture is better looking, because DDS does lose some detail with compression. However the mip mapping ability of DDS is the one pro that eliminates all of the cons IMO. I can live with a little detail loss for smoother performance. In TSOP i proved the point, because most of the particle textures were reduced in size by half, and converted to DDS, and all, but the most nit picky of players didn't notice any difference in game.

The jump texture runs less smooth because it is quite a 'heavy' animation, compared to most other effects in the game.