if ($code =~ /quoted-printable/i)
{
  print "printing $num to c:\\$filename\n";
  open(K, ">c:\\$filename");
  binmode(K); #not sure when to use this, seems to be necessary for pd
+f attachments
  print K MIME::QuotedPrint::decode_qp(join "", @{ $message->{body}->{
+data} });
  close K;
}
[download]

The error when trying to open the bad pdf is:
"The file is damaged and cannot be repaired."

Here's a snippet of a good one (note that in Notepad the
line-endings are little squares - \r I presume):

%PDF-1.2
%ßÜÂÞ - Business Objects
1 0 obj
<<
/Type /Pages
/Count 1
/Kids [ 4 0 R ]
>>
endobj
2 0 obj
<<
/CreationDate (D:20030206205259Z)
/ModDate (D:20030206205259Z)
[download]

And here's a bad one:

%PDF-1.2
%ßÜÂÞ - Business Objects
1 0 obj
<<
/Type /Pages
/Count 17
/Kids [ 4 0 R 5 0 R 6 0 R 7 0 R 8 0 R 9 0 R 10 0 R 11 0 R 12 0 R 13 0 
+R 14 0 R 15 0 R 16 0 R 17 0 R 18 0 R 19 0 R 20 0 R ]
>>
endobj
2 0 obj
<<
/CreationDate (D:20030206205456Z)
/ModDate (D:20030206205456Z)
[download]

Any advice would be great!

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.

I tried messing with the line endings, and ended up
with pdfs that open, but the content is missing (blank
documents). ??? Yet some work perfectly with no
manipulation of line endings. Thanks for the advice. I'll
keep plugging away...