As I pointed out in the comments, it is a problem with using closure variables in a loop.
Try
$("#runSimBtn").click(function runSimulation() {
$("#lContent h2").text("Simulation in progress...");
var agents = $("div.tooltipBox");
var falloutTimes = $(".rFO");
var i, j = 0;
for (i = 0, j = 0; i < agents.length, j < falloutTimes.length; i++, j++) {
var ttl = falloutTimes[j].value;
if ((ttl != undefined) && (ttl != 999)) {
(function (i, ttl) {
setTimeout(function () {
agents[i].animate({
backgroundColor: "#FF0000"
}, 500);
}, ttl * 1000);
})(i, ttl);
} else {
continue;
}
}
});