Sorry I cannot test the audio situation I have an earlier mm ver. But i have an idea.
"I have tried to work with pausing and the problem that I am encountering with pausing is that what ends up happening is the displaying of the disks is delayed and while the buttons are delayed they are not disabled, so it still allows that audio to become out of sync."
(a race condition - that is why I suggested simple waiting. i see no solution posted above so let me try again....)
The Front-End has it's own evaluator separate from the kernel. I'm thinking maybe that's where your split (and then race condition) occurs. Make sure all expressions effected are done by one or the other but are not split in-between both. See "FrontEndEvaluate" for more info. I'm thinking that because I beleive many new features todo with dynamic front end content have some level of integration with the new front-end evaluator.