Smart search doesn't index custom fields. I compared it with the custom fields at content component and there the custom fields are automatically indexed.
All the content from the custom fields are not searchable. Not from the build search function or from the joomla smart search seee also
http://www.jdownloads.com/index.php/support-forum.html?topic=11928.0
Both issues shall be fixed in next release 3.9.6. (or at latest with 3.9.7).
this seems to be fixed to me. :D
Thanks for the update. ;)