Now I think about it, the other thing that does this is PDF files. Which are also a gift from Adobe. I loathe Adobe.

Not in Safari or Chrome. More a fault of the Acrobat plugin I'd imagine.

Safari with the native PDF renderer still steals the two finger swipe that does the "back" function from browser navigation. The must be a "good reason" as this irritant persists into Lion.

Only when you click to focus on it.

Depending on your OS and browser, sometimes all you have to do is mouseover it to lose all focus, both keyboard and mouse. This used to happen to me a year or two ago, with Firefox and Linux I think.