This bug is simple enough:
Effect.SlideUp begins by saving the bottom position of the inner element:
var oldInnerBottom = element.down().getStyle('bottom');
However, when it comes time to reset the position after the effect has run, this is what happens:
effect.element.hide().undoClipping().undoPositioned().setStyle({bottom: oldInnerBottom});
effect.element.down().undoPositioned();
The old bottom position of the inner element is being set onto the _containing_ element. This results in bizarre behaviour, such as the element jumping back to its starting position after the effect has run. I've attached a patch which fixes the problem by transferring the setStyle() call to the next line.