Might it be possible it is CGI.pm that is doing it?   I see code in CGI.pm

    # set charset to the safe ISO-8859-1
    $self->charset('ISO-8859-1');
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The CGI.pm docs suggest that you can set the charset output in the header by using

  print $query->header( -type=>'text/html',
                        -charset=>'EUC-JP');
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but of course CGI::Application wants you to set headers using its routine

  $webapp->header_props(-type=>'text/html', -charset=>'EUC-JP');
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From reading the docs I believe you could also influence the charset in the header by using

  $query->charset('EUC-JP');
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Is it possible you are calling the CGI.pm header() routine yourself instead of letting CGI::Application handle it?   I don't understand how you are getting two "Content-Type" headers.   Let's see, you can tell CGI::Application to *not* generate headers by doing

  $webapp->header_type('none');
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Let us know what more experiments find out.