Okay this is my final posting on the matter of fps, I have spent DAYS! configuring my system - often doing the same things several times over in different ways just to make sure I haven't missed anything. I have ironed the fps problems on MY computer to be down to two possible culprits : 1, Not enought ram on video card or 2, Need a faster CPU/front side bus speed.
I have tried all the different combinations of settings of my control panel and all the possible combinations of options in the graphic settings of the game. Firstly the most obvious pointer is that there is VERY little difference in game fps with the different graphic settings. A second indicator is that overclocking my video card also makes VERY little difference to fps. However the fps on the first menu screen when the program first loads up - DOES reflect, logically, higher fps when setting graphics options lower. However this change is not seen when playing the actual game. The fps shown on the first menu screen seems to me to be a good indication of how your video card is performing - without having any of the cpu pressures of when the game is running. So effectively - if the games use of my cpu was optimised - I would see higher frame rates by reducing the graphics settings - or overclocking my video card. Whats happening is that the frame rate is being limited by cpu processing, so increasing the speed of the graphics procesing with lower settings or overclocking the card only produces minor increases - it tends to effect the max fps when theres not much going on.
My system spec is in my sig. I have an ATI x700pro 128DDR3 overclocked to 450mhz core - 950mhz memory. I have found that I get the max fps for my system from the following settings:
Bios: AGP aperture 128mb, I've tried em all! On X2 it actually made the game have less and shorter stutters when I set this to 8mb!! But not so here: 128 and 256 seem very similar but on 256 I sometimes get some texture corruption. I would recommend having it on AT LEAST 128mb.
I also tweaked my memory timings. And slightly overclocked my cpu!
ATI Control Panel:
Catalyst Driver :6.14.10.6525 (as shown in display-adapter-properties-driver. Don't know what Catayst Version number this is - It says driver version: 8.12 on the installation disk) - I found this driver to be about 3/4 fps faster than the catalyst 5.10, or the 5.7 which I also tried)
Texture preference: ultra performance (although "quality" is almost identical)
MipMap preference: ultra performance
AA: Off
AF: Off
TRUFORM: Off
VSYNC: Off
Catalyst AI: Low
Geometry instancing: Off
X3 Graphics settings:
Textures: Low
SHaders: Low
AA: Off
AF: Off
AQC: ON
Post processing: Off
I also disable all external non-essential processes before running the game. Also it seemed to run slightly better installed on my C drive, probably because it has slightly faster access times! I also have my swap file (vritual memory) on another drive.
With these settings I get the following fps:
Argon Prime (at start of game): 10-22fps (10 when looking at all the stations and busy parts - up to 22 when looking at the gate or other non-busy scene)
Home of light - 15-26fps
First khak battle in Home of Light - about the same, but with occasional stuttering when it gets particularly hectic or when the first few explosions happen)
I never hit 30fps though - unless I deactivate the HUD - whoopie - up to 38fps! Quite often I deactivate just the monitor as that tends to give me a 4 or 5 fps boost.
So the game is just about playable for me after some serious tweaking and trouble shooting. There is definately something going on with the access of the videos of people your speaking to in the monitor in the top right, it doesnt change person on time and it is also very jerky. Also as has already been said the sector map seriously hits the fps.
ALthough the above settings give me the best fps on my system I actually run the game with shaders on medium and texture preference in the control panel on quality. I probably loose about 3fps but the whole game looks sooo much better. I LOVE the shader effect on medium - on low it makes the ships hard to see and you don't notice the detail so much. ALso the textures on "ultra performance" in the ATI control panel do look a bit ropey!
I hope this helps somebody, it will make me feel better for spending so much time just configuring a game!

System SPEX: Athlon xp2400+ , 1 Gig DDR (333mhz), RADEON x700pro 128 DDR3 (clocked to 450mhz core, 950mhz mem with ATI tool) SIS K7S5A mobo (running at FSB 266), onboard AC97 sound (yuk!).