I take back my comment about not base-64 encoding. I just looked at my code and it says: 
  my $instances = $ec2->run_instances(
    ImageId  => $ami_id,
    MinCount => 1,
    MaxCount => 1,
    KeyName  => $key,
    (defined $user_data ?
       (UserData => MIME::Base64::encode_base64($user_data)) : ()),
    (defined $instance_type ?
       (InstanceType => $instance_type) : ()),
  #...
  ) or die "$ec2->{error}";

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-- Eric Hammond

In reply to Re^2: Net::Amazon::EC2 loses pound-shebang when base64'd by esh
in thread Net::Amazon::EC2 loses pound-shebang when base64'd by hesco

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