Well, I just found out that putting the player.shader file in my pk3 only helped the problem and didn't solve it entirely.
What I'm trying to do is add new shaders to all of the default skins in Jedi Academy. About half of the skins work with the shaders in multiplayer and I keep getting the same warnings for my shaders. Is there any way to make this fully compatible with multiplayer?
Any help would be appreciated as I want to finish this mod and start working on the JK2 version.