So, trying to narrow down the problem I wanted to verify that "scene" is in fact getting set:

#!/usr/bin/perl
use strict;
use warnings;
use Image::Magick;

unlink (glob("*.tif"));

my $image = Image::Magick->new;
my $filename = "test.pdf";

$image->Read($filename);
my $p = $image->Get('scene');
print "\n\nScene1: $p\n";

$image->Set(scene=>15);
$p = $image->Get('scene');
print "Scene2: $p\n\n";

$image->Write(filename=>"testp%04d.tif",
              compression=>'Group4',
              density=>"240x240");
[download]

My output is:

Scene1: 0
Scene2: 15
[download]

So it appears as if "scene" is being properly set, but that it's being ignored by the Write method.