PerlFreshRestart is a mod_perl 1.0 legacy option and doesn't exist in mod_perl 2.0. A full tear-down and startup of interpreters is done on restart.

If you need to use the same httpd.conf file for 1.0 and 2.0, use:

<IfDefine !MODPERL2>
    PerlFreshRestart On
</IfDefine>