> Does that help?

Well, the explanation was interesting and informative
and I was able to find and modify the code (adding a
trace as a sanity check):

   sub run_program {
     my $self = shift;

     die "No arguments passed to run_program()\n"
         unless @_;

     die "Must pass arguments to program '$_[0]'\n"
         unless @_ > 1;

     my $fh = $^O =~ /Win32/i || $^O =~ /VMS/i
          ? $self->windows_fork( @_ )
          : $self->real_fork( @_ );

     local $/      = undef;
     my    $output = <$fh>;

     close $fh || warn "@_ didn't run correctly";

     print STDERR "run_program was here!\n";      # DEBUG

     # When using IPC::Open3, need to reap the processes.

     waitpid $self->{pid}, 0 if delete $self->{pid};

     return $output;
   }

Sadly, I am not yet seeing any of the warning messages:

   ...
   run_program was here!
   Error (0): PDF file is damaged - attempting to
     reconstruct xref table...
   run_program was here!
   Error (0): PDF file is damaged - attempting to
     reconstruct xref table...
    run_program was here!
   ...

Help?  Clues?  Suggestions?

-r