Essential little thing you forgot to mention and I just experienced myself.
If you raise suhosin.post.max_vars you also need to make sure, that suhosin.request.max_vars is also raised to this new maximum, because otherwise it would overwrite the suhosin.post.max_vars.
I also raised max_input_vars from php to make sure really NOTHING keeps inputs from getting posted.
Code in vhost.conf (Plesk based ^^).:
php_admin_value suhosin.post.max_vars 5000
php_admin_value suhosin.request.max_vars 5000
php_admin_value max_input_vars 5000
Should work in .htaccess, too. But I have not tested it.
func0der
