This is similar to a problem I'm having with playing video. In my case, the video gets clipped at the end. I found that by publishing with the "Control Preloading" setting on "Disable pre-loading" (Rather than "Download slides completely), that the problem was minimized. Some slides, however, still clip the end of the video.
Sounds like a similar problem. Seems like Presenter has a disconnect between the playback of the vido/audio and the playback of the slide itself. It seems that the slide's playback is set to the time of the video/audio, but the video/audio and the slide timer play independantly when played.
I don't know if this helps, but I think that video slide playback cooordination problems exist, and I hope Adobe looks into it.