No it's just that 'alert'... the line looks like this: alert(wpm); ... that's the popup.
Try this: In Firefox go into some MooTyper activity and right click -> View page source
From there you can see if the script typer.js is included properly. If you click on it's url you will arrive directly on the script's code. See line 45 if it's there or not..
If the alert is there you still have some problem with cache... if not, there shouldn't be a popup.