I'm assuming you're using Beryl with Xgl. It's a common problem which hadn't
been totally fixed yet. There is a solution for VLC media player. Read these
posts:
http://ubuntuforums.org/showthread.php?t=287182
What I would recommend is stop using Xgl, at least for now. Edgy already comes
with AIGLX preinstalled with xorg-xserver. Beta drivers that support AIGLX are
available for download in case you have ATI or nVidia.