This issue seems to be back: https://www.jdownloads.com/forum/index.php?topic=11928
(Yes i know it is time to move to J4 ;D )
Some investigation:
The function
FinderIndexerHelper::getContentExtras($item);
is called, which what i understand should index the customfields.
I compared the jdownloads and content but do not see any strange differents.
Any ideas? Now my trick to search in de pdf content does not work. :'(