You have an all-white alpha channel in your -cl texture file.  Switch it to all black, which will cause the alpha channel to disappear upon saving.

Remember when you edit the texture file that it will open without an alpha channel, but saving in the dxt5 .dds format will automatically create a new one that is, unfortunately, solid white.

You will need photoshop or Gimp to edit the .dds files. And the Nvidia plug in. Open the texture files in photoshop and follow Myfist's great tutorial on textures. It's in the main Modding sub forum. It took me a few days to figure out but really it's not that hard . 

You don't need to rename the textures. The mesh file is looking for the and now can't find them. I took an advent frigate mesh and named it to the TEC frigate mesh and now the TEC have a perfect stolen design.

Find with Tau or Ork ship you want to replace in the mods mesh file. Then copy the TEC ships mesh file from the install directory (binary file) or the updated reference files (text file) and place it in the mod folder. Rename the TEC mesh to the Tau or Ork mesh.

[Tutorials] 3D Modeling, Texturing, Importing & Converting

myfist was just saying you don't have to rename the mesh and texture files to match what's currently in the game.  You can name them whatever you want, so long as they match up.  If, however, you are planning to replace entire factions of ships then I suggest you stick to the stock naming scheme.  There are other references to mesh names that can become a real headache if you don't catch them. 

To fix your problem, you absolutely must fix the alpha channel in the -cl.  Here's a link the the dds plugin.  Just follow the installation instructions, and you're set.  

I suppose that you're unfamiliar with the texture file system, so I recommend you do take some time to read through myfist's tutorial.  The various color channels in the -da file all have different but equally important functions (metallic shine, lighting, reflectivity, and bloom), and then the -nm map creates additional bump/3d effects.  The -cl file is strictly for the actual coloring of the mesh with the exception of that alpha channel. 

When using Gimp the alpha channel is the opposite. Team colour in the cl. file needs to be black and the rest needs to be completely transparent. as with the bloom in the da. file.

I'm pretty sure you can't edit channels that are dds. in gimp. So you will need to make a Png. file, edit the channels then convert it to dds. Gimp also needs a dds. plugin it can be found here;

http://code.google.com/p/gimp-dds/

No, sorry, the alpha channel in the cl file is for team colour. The places on your texture file where you want team colour to be will need to be black in the alpha channel and all else in the alpha channel where you don't want team colour needs to be transparent or white in the alpha channel for Gimp.

Pretty much all tutorials say that you need white for team colour in alpha but they refer to photoshop or perhaps some other programs. I don't know why but Gimp is opposite in regards to alpha channels.

It may well do so now. I still have an old 1.7 version of dds plugin. I may need to update.

If you made the whole channel black that is what would happen. You only need where you want team colour to be to be black. It only needs to be 1 pixels worth if you don't like team colour on your model.

To find what the mesh files are for their respective entity file, open up the ships entity file and go down to the entry

MeshNameInfo
    meshName

and that will give you the name of the mesh that that ship uses. It is towards the bottom of the entity file.