How To Use Count Down Timer

I have created a javascript count down timer to be used in asp.net. Basically, I create a countdown time for user to register (20 mins). If the countdown is around 5 min (that means the user is inactive for 15 min) then generate confirm box asking whether the session has to be active. If the user clicks ok, then we reset the time. If cancel is clicked, we proceed with the timer countdown till it reaches zero and logged out. IF he does not do any action, the countdown timer will proceed and logged out.

The problem is: Whenever the confirm box is popped up, the timer counter stops the counting. And If user does not click on either button and remain inactive for more than 5 min (by 5 min, the user should be logged out) there is nothing done that means, the counter stops countdown and the user is not logged out. Is there anywhere to determine in javascript whether a confirm box is popped up?