In other words, the code at http://www.nerds-central.com/Linear-Scan-Test.html looks like this code is using the antiquated setTimeout() method of determining frame rate.
A better way to do it, at least for chrome and firefox users, is to use the newer requestAnimationFrame() function: http://paulirish.com/2011/requestanimationframe-for-smart-an... This allows for the browser to notify the script when its ready to display a new frame, resulting in more efficient animation execution.
Using FPS for benchmarking is good, but suffers from the same shortcomings as glxgears.