http://www.vista4beginners.com/Disable-System-Beep
Couldn't test it, as my WaitWindow is behaving well.
Unfortunately the specific advice didn't work in my case (and I did a reboot and the beep remained disabled) but I did go into Personalise > Sounds and turned of all system sounds and that removed the wait window beep. So, it just a matter now of finding what what specific windows sound is being generated when the screen modality changes and disabling it.
So much to learn --- so little time!
Cheers, Peter
For the record - in my environment (Vista Ultimate) setting Personalise > Sound > Default Beep to None fixed the 'problem'.
I am glad you found a way to sort of fix this, but there should be something deeper than that since I also have Vista Ultimate and the settings of Default Beep for me is the default one, and I have never seen the wait window causing a Beep.
This isn't 100% in all environments. There are a lot of factors that can come into play here, that is why I pointed out that I could not reproduce this on all machines. But it has to do with modality and the beep outside of that dialog. If I ever get this reproduces on my development machine I will try and come up with a workaround that doesn't involve changing anything.