<Location /perl>
    SetHandler perl-script
    PerlHandler Apache::Registry
    Options +ExecCGI
    PerlSendHeader On
</Location>

print "Content-type: text/html\n\n";

If this is the case, you must make sure that you have:

PerlSendHeader On

in the configuration part of the <Location> section:

<Location /perl>
    ...
    PerlSendHeader On
</Location>

This adds a little overhead to the output generation, because when this configuration is enabled, mod_perl will parse the output and try to find where the header information ends so it can be converted into a proper HTTP header. It is meant only for mod_cgi emulation with regard to HTTP headers.