I\'ve got a large form and I can see from firebug that all of the elements\' values are being sent properly, but when I print_r($_POST) there are only 1000 variables display
I see what you did here.
max_input_vars, 1000
Introduced in order to prevent hash collision attack: http://www.phpclasses.org/blog/post/171-PHP-Vulnerability-May-Halt-Millions-of-Servers.html But failed in 5.3.9: http://www.phpclasses.org/blog/post/175-Another-Serious-Security-Bug-on-PHP-539.html So you should update to 5.3.10+ if that is problem.