After further investigation of my problem, I found that if I tell a bone to play an animation, it for some reason stops being animated all together. So let's say I do "PlayAnimation(1, 0.5, 100, 0)" on the neck bone, it just ceases to animate all together which allows me to do things like rotation on it. While this is sort of useful I imagine this isn't the intended effect (and that this is what the StopAnimation() function is for)
Either this is a bug in the current version (4.6 as far as I'm aware), or it's a bug in my project because I originally started it in the demo which is only running 4.3 (or at least says it's running 4.3).