Wordpress Menu Item Limit

I have my running website up and everything was going smoothly until I hit a max menu item limit. I have been scouring the web for the past week to remedy this issue without any luck so far. I have tried the following.

Edit /etc/php5/apache2/php.ini by changing max_input_vars from 1000 to 3000 or 5000. Restart apache

Create a new php.ini and put in wp-admin folder.

Change max_input_vars = 3000 upload_max_filesize = 70M; post_max_size = 128M; upload_tmp_dir = 70M; max_input_vars = 3000; memory_limit = 256M;

edit .httaccess by adding <IfModule mod_php5.c> php_value max_input_vars 5000 </IfModule>

None of these have working for me. I am using the ubuntu 4 wordpress image - there must be something server-side that truely controlling the max_input_vars.

Thoughts, suggestions?