Every time I have a flash movie in a slide and i change the slide, I expect
the flash movie goes "under" the left and right margins of the slide. I
see, instead, that the flash movie overlaps above the margins and is
visible while the slide changes.

It happens also in your demo at
http://www.missingmethod.com/projects/glider.html
in the fourth slide

I'm using 0.0.3 version (with the patch to show active links), both on Mac
OSX 10.4.10 (FF and Safari) and Win XP (FF and IE7)

I tried also to use the wmode="transparent" param in the swf embedding
code, but without results.

Probably is a flash issue, combined with the slide effect.
Is there a way to fix this?

However, a great script!
Thanks,

Claudio