You probably just timed it right to get that behavior, bigbox for example, shrinks on hover, other themes will fade or whatever. If you are 'hovered' it will continue the animation at whatever point you were at when it goes to close the notification.
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I think you should change the default template to libnotify, so much nicer.
Also, the notifications behave strange when hovering over them with the mouse... they shrink onhover, then on the next hover they dismiss.
This is on Chromium 15.
You probably just timed it right to get that behavior, bigbox for example, shrinks on hover, other themes will fade or whatever. If you are 'hovered' it will continue the animation at whatever point you were at when it goes to close the notification.