My guess is that you have /usr/bin/perl (Perl v5.8.8) with libraries stored in /usr/lib/perl5/site_perl/5.8.8/…, and then you also have /usr/local/bin/perl (Perl v5.13.9) with libraries stored in /usr/local/lib/perl5/site_perl/5.13.9/…. When you updated File::Spec, you updated the version used by /usr/local/bin/perl, but /usr/bin/perl is still using the old version.
You must either update the version of File::Spec used by /usr/bin/perl or make Apache use /usr/local/bin/perl.
To update the version used by /usr/bin/perl you can use
/usr/bin/perl -MCPAN -we 'CPAN::Shell -> install("File::Spec")'
I don't have much experience with Apache, but I am sure there are several ways to make it use /usr/local/bin/perl. You could try to place /usr/local/bin before /usr/bin in the PATH environment variable, but that might have other consequences, though.