It's usually best to post a test case.

Perhaps the module defaults to writing to a tty that you're not getting in the cron environment.

Are you doing this type of thing? I just lifted this from the module docs.

 # how we create some handles to interact with GnuPG
  my $input   = IO::Handle->new();
  my $output  = IO::Handle->new();
  my $handles = GnuPG::Handles->new( stdin  => $input,
                                     stdout => $output );
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