I worked with flags before, but not with units like you describe it. I think that non-decal flags need a <bWhiteFlag>1</bWhiteFlag> (or at least they should work with that as otherwise that entry would be very limited in sense...). If the units flag works like a non-decal flag, you should try to set the WhiteFlag to 0. This could cause troubles to your civs flag if it is a decal flag, you would have to replace it by a non-decal then.
If you like to change the units shader, you may try around with nifskope (not nifviewer / sceneviewer). Open your unit in nifskope, select the mesh you'd like to alter (simply click on the model in the 3d view). If it is not already set, set the view to tree-mode. You will now see the parent-child relations between the nodes on the right in a similar way like the windows explorers view. Your mesh should still be selected. At the bottom you can see the meshs properties, or at least some of them. There should be a property called "hasShader". There you can switch of the shader. There is also a property near, giving informations about which shader is used. Theoretically you could enter another shader here, but I never tried that out so far and sometimes things don't work as one could think.
Now "open" your mesh by clicking on the + on its left in the right tree view. Now you should see all the children of the mesh. Search for the TexturingProperty. Again, open it by clicking on its +. The TexturingProperty should have at least one SourceTexture child. These SourceTextures represent the maps that the mesh uses. That means one should be the texture itself (that's the one that should be there anyways), others are shader related (gloss for example). Take some time, you should find out which SourceTexture is which map. Write down the id of the node of shader map you'd like to remove. Back in the TexturingProperty search for the Num Shader Textures and the Shader Textures properties (again, list at the bottom). With the latter you can disable certain shader files. You'll need to know the id of the shader maps node to see which shader texture is the one you want to disable, which is why I told you to write it down. I think nifskope will keep the SourceTexture for a while. Once you save your nif, close it and reopen it. The SourceTexture node should now be gone. So, AFAIK there is a shader map that controls the player colour. If you remove that, you may get rid of your problems, but it can get even worse, too. You'll need to try around with these properties. Or maybe you'll have to try a lot. I don't know.
As you see I can't give you clear advices how to fix your problem, but maybe you will find your way by your own with the information given here. Good luck!
