It sound like maybe the PDF reader is very critical about line endings. On a windows platform a line ends in \r\n while on *nix platforms a line ends in just \n. It could be that the quotedprintable decoder messes up the newlines.
Although i do not have a clear answer for you, you can test this more by substituting the line endings in the bad pdf with other line endings:

my $pdfContent = MIME::QuotedPrint::decode_qp(join "", @{ $message->{b
+ody}->{data} });
$pdfContent =~ s/\n/\r\n/g;
[download]

Play a little with the line endings and test it.