Alpha didn't add the javascript functions which create new, additional child "clock" loops every time you cycle through the parent "refresh the list" loop.

Try this...

In your startTime function, add:
console.log('runtime: '+runtime);
right before the line of code:
var t = setTimeout(startTime, 500);
In your onTimer code, add:
console.log('onTimer fired');
before the line of code:
Without creating a PhoneGap app, open the app in Chrome. Do an "F12" or Right click "Inspect" on the page so that you see the console.
Now click on your app's "3 secs" button and watch the console for awhile....