Well, here's how I got it to work. I had all shaders for each character assigned to their own shader file (i.e. Kyle's shaders were in a Kyle.shader file). So what I did is compiled all of the files into the players.shader file which is in the assets1.pk3. Made sure every shader was spaced correctly and it worked like a charm. Works in the default multiplayer, JKA+, and Moviebattles. I'm sure it works with any other multiplayer mod out there too.
Still have to finish shaders for the ships and vehicles and this mod should be done. Then I have to whip up a JK2 version and both versions should be out soon.