If you're using CGI.pm, try using the :unique_headers option. This will prevent a CGI object printing more than one http header.

Example:

$ perl -e 'use CGI qw/ :unique_headers /; $q = CGI->new; print $q->header, $q->header'
Content-Type: text/html; charset=ISO-8859-1

$

If this fixes the problem, you should probably still have a look through your code and figure out where the redundant header is being printed.