Hi Tachyon,
I figured out the problem. For pdf files at least, the quoted-printable format was missing an "=" at the end of one or two lines. So, when I ran it through the MIME::QuotedPrint::decode_qp, the extra control-M (\r) was getting stripped. I'm not sure why it works, but I'm doing a s/\n$/\r\n/ on lines that don't end with =.