I just realised it seems to not be archiving any of the 20 sites I have on there either..
I've temporarily defined $PIWIK_SUPERUSER and $PIWIK_SUPERUSER_MD5_PASSWORD directly in the code and still no luck.
When it executes;

$TOKEN_AUTH= & $PHP_BIN -c $PHP_INI "$PIWIK_PATH" "--" "module=API&method=UsersManager.getTokenAuth&userLogin=$PIWIK_SUPERUSER&md5Password=$PIWIK_SUPERUSER_MD5_PASSWORD&format=php&serialize=0"

it returns a token, but something is wrong as it thinks the superuser isn't a superuser :-(

Are you sure about your super user token? when you execute this in the browser with the same token_auth as you use in the archive.sh, does it trigger archiving?

Probably unrelated, but the script should use the -q flag so that php-cgi doesn't emit the HTTP headers.

(In [3705]) refs #1959 - use -q flag in case php.exe is the cgi binary

Have you tried with the -q flags (as per previous comment) please let us know

no update for 2 months, assuming it is working...

In 916d8d6: Starting January 2014, this script is now deprecated. Please only use the standard archive.php script in your scheduled task setup. See documentation at: http://piwik.org/docs/setup-auto-archiving/ Refs #1959 #1411 #2848