Hello,
if the metada were present in JoomSEF, but not visible in the page source, then either JoomSEF metabot is not working correctly from some reason.
Or there is conflict with some other component / plugin that is overriding the metas generated by JoomSEF.

You could try debugging it with checking if the metabot is working fine. (the coflicts could be tested by switich other plugins off one by one)
At some sites, the TRIGGER on which JoomSEF plugin is stated was not initiated corectly. (error in index.php file in some of the previous Joomla versions) So also make sure, you have your Joomla up to date to the latest version.