Sorry for the delay.
Are you using the Spine runtime that comes with cocos2d-x or the latest from our official GitHub? If using the official runtime, are you up to date? If so, I'm not sure what to say. It could be that something you are rendering changes the GL state and then subsequent rendering goes bad. Maybe try disabling/removing things from your scene to narrow down what is causing the problem, and/or create a very simple example to see if it also has the problem.