I have tried it with compositing on and off, and even tried using Lubuntu, which has no compositing. The computer I have been testing on has Nvidia graphics. I have tried using both the Nvidia and Nouveau drivers. I have run the tests using Ubuntu 12.04, 12.10, Kubuntu 12.04, 12.10 and Lubuntu 12.04, 12.10. I'm not sure why it seems to work properly for you and not me.
My church does not use the alerts, but would not want to take them away from someone else.
We do use video extensively. We are a small congregation and use videos for all the praise and worship songs.
Is it a stacking issue (z-order)?
Finally, the computer I am using has an AMD Phenom II X4 processor.