You could try a good, old-fashioned setTimeOut. Move the last part of your code into a separate function and have it call-back after a second or so. 

function onSubmit() {

var req = g_form.getValue('enter_your_vsa_request_number_to_get_started');//this is a reference field to the [sc_request] table
var URL = "itc?id=sc_request&table=sc_request&sys_id="+req;
alert('You will be directed to the Selected Vendor Assessment Request. Please click OK.');

top.window.onbeforeunload = null;//this removes the popup that asks if you want to leave
setTimeout(sendOff(URL), 1000);
}

function sendOff(URL) {
top.window.location = URL;
}

That seems to be working every time for me...

If this was helpful or correct, please be kind and remember to click appropriately!

Michael Jones - Proud member of the CloudPires team!