nah, that title doesn't really sound like what the problem is...ah well...anyway

I placed a few MD3s into a multiplayer level of mine, and for some reason only some of the textures show up on them, namely the animated ones specified in the shader. the rest of the MD3 is covered in black...is there any way to fix this or am i stuck not using the model?

Well I've had that problem too. All the times it's happened it's gone away for some reason the next time I start up the game. Take a look at any error messages that pop up (shift + ~), and it might give you an idea.
second if you didn't extract all the textures you'll have a problem I think. Though I'm sure you did.

extract them from assets0.pk3? (or whatever that file is called)...oh...no...why would i do that? i'll try it though, thanks