use total_ticks instead:
Code:
var count,ms,sc,mn = 0;

function count_up() {
	var start = total_ticks;
	while (1) {

	count = (total_ticks - start) / 16 * 1000;
	ms = integer(cycle (count,0,1000));
	sc = integer(cycle (count / 1000,0,60));
	mn = integer(cycle (count / 60000,0,60));

	wait(1);}}