Whatever Perl you're using for your browser script is not the same as the one you used when installing Digest::MD5::File.

Not necessarily, /root/perl5/lib/perl5 makes it look like OP used local::lib under root to install the module. shmem already noted some of the problems with that, although I agree with your advice not to modify the system Perl, at least not with cpan or cpanm - using the system's package manager is usually okay.