Ah thanks so apache prints the content and then appends its own 404 document to it.
Must be an apache config thing then.
Huh? You didn't say this was the problem :/
If you want to avoid ErrorDocument getting appended, see http://search.cpan.org/~gozer/mod_perl-1.31/faq/mod_perl_faq.pod#So_how_do_I_use_mod_perl_in_conjunction_with_ErrorDocument%3F