In the handleTimer method in the CPMCTICallTimer there is this code:

if(typeof serverClientTimeDifference != "undefined" && serverClientTimeDifference)
   oTimeComponents = cti.util.Timer.getTimeComponents(lCurrTime - this._lStartTime+(serverClientTimeDifference));
else
   oTimeComponents = cti.util.Timer.getTimeComponents(lCurrTime - this._lStartTime);

 this._oActionHandler.handleTimer(oTimeComponents);

You might note the time when you switch away from the active tab and introduce a new variable to "this" which contains the time you switch away, say "this._timeSwitchAway".  Then, when you enter this same bit of code again, look to see if this._timeSwitchAway exits, and if it does, add to the start time "currentTime - this._timeSwitchAway."  Then clear this._timeSwitchAway.

For example, if the timer started exactly 1 1PM, and at 1:30 PM you went to another tab for 5 minutes, this._timeSwitchAway would be 1:30.  If you came back at 1:35, you would compute a 5 minute differential, and add it to the start time, so the new start time would be 1:35.  In essence, you eliminated the time spent switched away.

There will be  a few details that you'll need to figure out (i.e., how to determine when you are leaving the current tab), but I think this will work.