I am using CM Partners. One of my partners with a claymore has recently taken to killing the other in one stroke of his blade. Every time the other guy wakes up again, the other NPC kills him again. Is this due to some disposition issue? How do I fix it?

You can still open the .esp of the specific CM Partner in CS. If they are not already in the PlayerFaction then add it to them all. This alone could solve the problem. Also, check their Aggression. IMO it should be 5 or else they may go aggro on someone merely for having their weapon out.

Check out the link in my sig.

It sounds like a friendly hits problem. Friendly hits is set to 3 by default but I raised it to 20 so that its less likely that companions will turn on you or eachother.

Try the mod in my sig and the problem should be solved.

Cleared my problem right up. Question is, though, what happens after my companion hits the other guy 20 times? Or does the counter reset every 3 days?

If that happens... if...

then they will fight like before but I think it resets after the battle music stops or sometime after a fight.

I say 'if' because the likely hood of a fight is so small that you never see it happen anymore so you don't have to worry about it.

Ah, I see.

Never mind, the two are still trying to kill each other. Is there a way to reset an NPC's disposition?

Companion Rings will fix it.