I am having issues with code still running after it has been commented out, and not executing the replaced code. I've tried clearing the browser cache but no luck. Is this a PHP or a FuelPHP issue?
More than likely your not uploading your code to the right place and the old version of your code is running. To make sure, change something in the HTML so you can see whether your changes are actually taking place or not. Also, you can look at the modification date of the files on the server to make sure it is changing.
If this doesn't solve your problem, you might have caching on the server. Try restarting apache.
If there really is a problem with comments not working correctly, it would be a PHP bug, but I find that highly unlikely.