If you're running on Windows (assuming you are), you can use the WindowsShell object to exec the script. This will run the script in the background, without opening a command window on your desktop.
$shell = new COM("WScript.Shell");
$cmd = $WshShell->Run("c:\php\cli\php.exe c:\yourscript.php", 0, false);
Under the CLI version of PHP, scripts have no max execution time.
If you just need to run a PHP script and don't care about going through a web browser to get there, just run the script directly, using the CLI version of PHP.
If you're on a UNIX system, use exec(). Same idea.