Are you running Beryl on Ubuntu? Do you have the problem where dialog boxes or new windows open under your existing window? This is most noticeable when web browsing, and coming across password-protected pages. I’ve been annoyed by this bug for about a month now.
It turns out, this is not a bug, it’s a feature. Beryl has a setting called “Focus Stealing Prevention”, designed to keep windows from stealing your focus. This is great if you really need to concentrate; it’s annoying if you need to find the password dialog box before proceeding.
To fix, open up the Beryl Settings Manager, and click on General Options. In here on the Main tab, you should find an option for “Level of Focus Stealing Prevention”. This is probably set to “Extreme”. Switch this to normal and voila — your windows should behave normally again.