Please go to theme folder, create php file with phpinfo() function inside and send us link to that file so we can have a look on your server settings. We will see if above settings are real because in 99% cases, hosting providers are trying to cheat us with with simple changes in .ini files that are not real.
Ok, thanks. So just as we thought, your real values are far from what you presented above. The first thing you supposed to start from is disabling SUHOSIN extension because this the reason why you can not add more elements into builder.
Comments
sounds like you are unable to save the content only because of the limits on your server side. More details about that you can read in the following topic http://forum.muffingroup.com/betheme/discussion/7689/muffin-builder-items-or-page-options-can-not-be-saved-max-input-vars
Thanks!