[ShaneC]

If you combine it with what I already suggested. I really don't want to do too much in the way of coding for you here. The point is that you need to learn, otherwise if this breaks down you'll have no way to fix it or even modify it.

In your jQuery AJAX you put a condition:

var refreshCountdown = 	setInterval( function() {
						$.get( "/ajaxTimer.php", {}, function( data ){
							if( data == "Database Backup in T-Minus 0 minutes 0 seconds!" )
								$("#backupCheckbox").hide();
							else
								$("#countdownBlock").html( data );
						});
					}, 1000 );