Hi,
Although I haven't done extensive testing yet, here's one thing about Flash 10 our team has discovered: Flash 10 has improved, upgraded audio functionality which plays audio clips more efficiently- although this may sound great, what it means is that courses that looked great in Flash Player 9 (and prior versions) may experience some latency (what's actually happening is the clip is playing more efficiently) and therefore animations can sometimes go out of sync. The solution we've found is that higher quality audio clips don't seem to encounter any problems.
The trick then is when publishing your Presenter course to set the audio quality to "High" under the course's Preferences (Adobe Presenter>Preferences, Quality tab). This will save them at 24 kbps rather than 16 kbps. It's important to note that Presenter's default setting for audio quality is "Medium" (16 kbps), so you'll want to change this setting for each new course.