although i haven't tested, this looks suspiciously like a case where binmode might be necessary.

as it stands, it can also be written as a one-liner, like

perl -000 -MDigest::MD5=md5_hex -ne"$\=md5_hex}{print" your_file_here
[download]

note the triple-zero option to undefine the output line seperator.

~Particle *accelerates*