It seems that it has to do with the lack of a predefined height and overflow. Also the use of margins and padding also skews the animation. Have a look at this for a working example.
$(".alert .close").click(function(event){
$(this).parent().css('height',$(this).parent().height()+'px');
$(this).parent().animate({
"overflow":"hidden",
"border-top":"none",
"border-bottom":"none",
"padding": "0 15px",
"margin":0,
"height": "0px"
}, 400);
});
This will ask zepto to calculate the current height of the element so that we can animate it to 0.