Most essential detail is missing in your question. HOW are you playing the audio? From your description I can guess that you attached the audio to the button as object audio. If that is indeed the case, it is normal that the audio plays when the button appears. If the button appears from the first frame of the slide it will indeed play from the beginning of the slide.
If you want the audio to play only when it is pressed, you need to use the command 'Play Audio' eventually combined with other commands in an advanced action to be triggered by the Success event of the audio. Do not use any other type of audio.
I am confused by your statement about hidden timelines. What do you mean, please? If you hide an item in the Timeline panel, that will not be reflected in output at all. Maybe have a look at this blog post: