Maybe you can add your code another condition to break it..

if (seconds == 0 && 0 == minutes){ break;}

Code:
#include <acknex.h>
#include <default.c>

var milliseconds = 0;
var seconds = 10;
var minutes = 01;

PANEL* pan_time =
{
	pos_x = 740;
	pos_y = 5;
	digits(200, 70, "min: %0.f", *, 1, minutes);
	digits(100, 90, "sec: %0.0f", *, 1, seconds);
	digits(100, 110, "msecs: %0.f", *, 1, milliseconds);
	flags = SHOW;
}

function myTimer_startup()
{	   
	while (minutes >= 0)
	 {
	    milliseconds += (timer() / 1000);
	    if (milliseconds > 1000 && seconds > 0)
	    {
	      milliseconds -= 1000;	      
	      seconds -= 1;	      
	    }
	
	    if(seconds == 0 && minutes > 0)
	    {
	      minutes -= 1;
	      seconds = 10;	
	    }	   	    
	
	    [b]if (seconds == 0 && 0 == minutes){ break;}[/b]
	    wait (1);
	 }	
	
	milliseconds = 0;   
}

void main()
{
	video_set(1024,768,32,2);
	myTimer_startup();
	
}



Tested... :-)



Can't is not an option™