Program execution in any language, not just JavaScript, is not realtime. It will take a tiny amount of time to actually run the code to increment your counter and update the view, and that throws the "timing" off.
Additionally, many browsers have a "minimum timeout" length, which varies between 4 and about 16 (the latter being the computer's own clock timer), which will really mess with your code.
Instead, you should use delta timing.
var startTime = new Date().getTime();
setInterval(function() {
var elapsed = new Date().getTime()-startTime;
// update view according to elapsed time
},25);
If you're worried about it looking choppy, consider using requestAnimationFrame
instead, to update the timer exactly once per frame - this has the added benefit of not updating when the user switches tabs (but it will still be timing them) because if the tab is not active then there's no need to redraw stuff.