Sometimes while trying to activate Mega Menu checkbox unchecked after menu save.

If you enable debug, you will see the following error:

PHP Warning: Unknown: Input variables exceeded 1000.

You can fix this in 2 ways:

1. Remove unused menu items
2. If you need to have all menu items, you need to increase PHP value max_input_vars. By default on the most of hostings used 1000 value, you can try to increase it to 3000.

Add the directive into php.ini or place following lines into .htaccess:

php_value max_input_vars 3000
php_value suhosin.get.max_vars 3000
php_value suhosin.post.max_vars 3000
php_value suhosin.request.max_vars 3000