PHP Warning: Unknown: Input variables exceeded 1000

There is two way to solve this problem.

.htaccess

php_value max_input_vars 10000

php

ini_set('max_input_vars','10000' );

That's a new setting / value in PHP (related to a security update to prevent attacks to PHP scripts), so you get this after the update (before PHP 5.3.9 not set/available, suhosin users have a similar thing since ages).

Input values are of different kinds and array members count as well. So it's not enough to count form fields but also to take a look into the URL and other places related to input ($_GET, $_POST, $_SERVER, $_ENV, $_FILES, $_COOKIE ...).

See max_input_vars:

How many input variables may be accepted. Use of this directive mitigates the possibility of denial of service attacks which use hash collisions. If there are more input variables than specified by this directive, an E_WARNING is issued, and further input variables are truncated from the request. This limit applies only to each nesting level of a multi-dimensional input array.