Oh hai
I haz solvez your problem
but let me give an explanation first.
What you're basically trying to do is fit a nebula texture into a tiled skybox. Tiling suits extremely well for starfielc because stars are basically dots, so the likelyhood (and notability) of dot getting on both sides of a seam in the UV mapping is very small. That's why the tiling seams aren't notable at all on the starfield, but when you fill the texture with gradient nebulas, the likelyhood of getting completely different shades of colour on both sides of the seam is very high.
Ideally, for a nebula you would need a skybox that maps one texture spherically to the skybox. Nebulast typically stretch extremely well (well, in TGA format anyway - DXT compressed, not so much) so resolution isn't much of an issue - 2048x1024 is sufficient, but I prefer 4096x2048 since my GPU can handle it easily.
However, starfields love tiling. That's because when you stretch a dot, it becomes a blob, and stars do not like being blobs, they become stupid looking. Tiling removes the need for any significant stretching, thus tiling the starfield is a good idea.
The solution was to use two different spheres with different texture mapping. Outer shell with tiled starfield (got that from MediaVP's) and inner shell for spherically mapped nebula texture (spherical UV mapping was no problem at all after planets...); the minor difficulty I had was in TS3.2 to get the models' centers aligned and both spheres textured with appropriate mapping and texture. Well, it worked all right. Here be results.
...yes, the effect you were trying to accomplish looked familiar so I thought I'd give you a hand.
The skybox itself can be used for various types of nebulas and starfields of course, just by copying the model and renaming the textures in PCS or PCS2 (or heck, even Notepad++ has worked for me on some occasions...).
The trick is to make black transparent on the nebula texture, so the starfield gets through it. Making the nebula texture so it appears seamless is
bloody difficult, though. Polar distortions arent' really a problem, it's the horizontal seam between two halves that is really hard to blend into each other seamlessly...
As for the difference in using the background nebula system and a global nebula texture - the main advantage of nebulas is ease of use, the main advantage of global nebula texture is you get a seamless huge global nebula. Trying the same with the nebula system would get arduous and getting the different nebulas to match each others' edges seamlessly would be even harder than making this kind of nebula texture.
So, this kind of nebula is possibly better solution when you want a big, global, structurally relatively uniform nebula/dust texture - if you have someone who's able to make a distortio-less spherically mappable nebula texture, that is.
Nebula skybox is downloadable here.
If you want a different nebula, copy the model file, open it in PCS and edit the nebula texture to read something else (your specified nebula texture)... or just replace the skybox_nebula.tga with your own texture.
The model works well with either the provided, high-res 4096^2 starfield (my preference because I often use narrow fields of view) or the mediaVP starfield0001.dds, whichever you want to use. If you want to disable the provided, huge starfield0001.dds, just rename it to starfield0001_disabled.dds, and the model will then use the starfield0001.dds in the mediaVP's.
If your video card doesn't support 4096^2 texture size, resize the nebula texture to 2048*1048 and save as TGA.
...why TGA instead of DDS? Because DDS* dislikes gradients with passion, and stretching a DDS compressed gradient-rich texture will unavoidable result in ugly pixelation which I for one don't want to see.
I rather sacrifice a tiny bit of performance to the god of quality.
*Actually, it's badly done DXT* compression that hates gradients (and I don't know how to make it work properly), but I'm unsure if uncompressed u8888 DDS files have any memory efficiency advantage over uncompressed TGA's. I would think not, and RLE-compressed TGA saves at least tiny bit in filesize if not in memory consumption.
EDIT: This particular nebula pattern might not be what you're looking for - it certainly doesn't form the line of Milky Way - but with the technique I used it's pretty hard to have significant amount of control over the locations of the nebula concentrations. But as far as getting things to work, this kind of skybox model would most likely be what you're looking for. I'll leave you to either make your own nebula texture for the model, or use the one I provided.
EDIT2: MediaFire link changed to FreeSpaceMods link.
