Sometimes custom fields fail to save. As a possible solution you can try and increase the max_input_vars which was introduced in PHP version 5.3.9. The default value for max_input_vars is 1000, which means that if your form has has more than 1000 inputs, any additional values will fail to save.
You can increase max_input_vars via your php.ini file:
max_input_vars = 3000
or via .htaccess document:
php_value max_input_vars 3000
And as always there is of course a plugin available that can help in checking your PHP version and editing your php.ini file.