Could there be some subtle difference in the keys? Does it work if you put it in a foreach my $key ( keys %pdfs)?

Is there an extra layer of hashing you glossed over in the Data::Dumper output? (I know it's a rude question, but I've done it...)

Can other apps get the data out and read it correctly? You might be able to test this by piping the output from the command-line query parser (with some creative flags) into your PDF viewer.