i've never been able to use fixed positioning with interactive elements (audio, video, buttons, etc) in ibooks. apple's ebook forums are full of people searching for the same thing, but i've never encountered a success story there either.
with the particular issue you're having, it may be good to know that an audio/video element will stop playing once you leave the html page it's on - i mention this because it seems from your original post that you only wanted media to stop playing on page-turn.
if you're able to structure the book in such a way that the media is isolated on certain html pages (like if you're using it as intro-media attached to a chapter beginning for example, rather than embedded half-way through a paragraph), then this might be a solution.
otherwise, there's not really much i think you can do, but if you do find a 'fixed' solution i would be really interested to hear!