It seems to me it's your line endings...

echo -n "a" | md5sum gives me the same thing as md5_hex("a"). "a\n" and "a" should not hash to the same thing.

• "a" should be: 0cc175b9c0f1b6a831c399e269772661
• "a\x0a" should be: 60b725f10c9c85c70d97880dfe8191b3
• "a\x0d\x0a" should be: 0c629e1d3acda389c88a213374ec62fc

It's also worth noting that Digest::MD5 really is C, as much as /usr/bin/md5sum is: MD5.xs.