This might indicate a server related issue, but impossible to tell without actually seeing the code.
I remember someone had a similar problem a long time ago, and it was caused by an incorrect configuration in the php.ini, where the max_input_vars PHP directive was set to a low number, and not all the options were posted.
You can try adding the following lines to the .htaccess file in your root directory, but it might not work:
php_value max_input_vars 3000
You will probably have to check and change the php.ini configuration file on your server as well, to confirm if the max_input_vars value is indeed set to a lower value as the default 3000.Best,
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