You may have found a workaround, but I'm still curious to why it doesn't work... For some reason, CGI.pm isn't outputting proper linebreaks (preferably CR+LF) as it should... If it's a bug, I'd like the maintainer of that module to be warned.

Judging from the module's code, that is defined by the global variable $CGI::CRLF. Can you check what it contains — on the server, of course?

use CGI;
print "Content-type: text/plain\n\n";
print join " ", unpack 'C*', $CGI::CRLF;
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Except on EBCDIC systems, it ought to look like

    13 10
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