This should be how it works even now.
We have a test setup that makes Spineboy walk, run and idle, and have him shoot and aim his gun. It's currently working correctly.
Here; walk, run and idle are played on track 0. Then the shooting animation is played on track 1.
There was a recent change where non-animations no longer automatically end.
So where you used to just say:
SetAnimation(1, "shoot", false);
Now you have to say something like:
animationState.SetAnimation(1, "shoot", false); // This will play indefinitely unless you queue it to fade out
animationState.AddEmptyAnimation(1, 0.2f, 0.1f); // Queue a fade out 0.1f seconds after the previous animation finishes, mix duration is 0.2f.
Can you show a sample where it's not working correctly?