Be concerned with the scope of your variables and clear the blink intervall before initiating a new one.
$(document).ready(function() {
var refreshRate = 5000;
var blink = -1;
var autoRefresh = setInterval(
function () // Call out to get the time
{
$.ajax({
type: 'GET',
success: function(data){
document.getElementById('data').innerHTML=data;
if(blink>-1) clearInterval(blink);
blink = setInterval (function () {
var blink_cell = $("#blink_div").html();
if (blink_cell > 0) {
$("#blink_div").toggleClass("blink");
} else {
$("#blink_div").addClass("invisible");
}
},500);
} // end success
}); // end ajax call
}, refreshRate);// end check
}); // end ready