The popup problem only occurred after switching to an empty desk, and would go away as soon as you opened a window. (so it could never take focus away from a regular window) iirc, it has also been fixed in 1.01.

RabidVWM can change focus:
- while switching desktops, or a little afterward
- when a window is opened/closed
- when something asks it to (eg, taskbar)

I don't believe there are any times when it could change focus like this on its own, and I've never had any reports of such behavior.