Lag with nebulas warp points etc

What OS are you running?

For now, it sounds like a possible video card issue.

Only a few possible things I can suggest right now as far as troubleshooting.

1: Run the DirectX Diagnosis tool and check graphics related stuff.

2: Check to see if your video card drivers are up to date, although it is possible a newer driver lacks funtionality in previous drivers.

3: Try out other games with 3d graphics and similar requirements and see if they also experience similar problems.

Other factors:
Number of ships/units could be a factor also.
Does the lag always happen, or only when there are quite a few ships/units in battle?

If you have Windows Vista, I've heard it and SE V don't always get along well.

I happen to have an Nvidia 6200 w/ 256mb myself, but I have little noticable slowdown in a battle in a storm.

One possible fix if you can find no apparent problems.
On the SE V front end, check Setup and see what your display settings for the game are.
There are a few things that might improve performance.
Such as reducing the Video Mode to a lower resolution, making sure the proper Display Driver and 3D device are selected, and even see if lowering Graphic/Background detail setting.
Not sure if Video Memory Usage would help or not, since I am a bit clueless about that one, but it does have a 'safe' option for it, which sounds like it might be handy in some situations.