I'm pretty sure that is indeed the cause. Here's a test using md5sum from Perl: 
open OUT, '>', 'tempfile';
print OUT 'a';
close OUT;
system('md5sum', '-b', 'tempfile');

[download]
Result: 
0cc175b9c0f1b6a831c399e269772661 *tempfile

[download]
So yeah, md5sum and Digest::MD5 agree.

It's the OP's other tests that were flawed.

In reply to Re^2: Exchanging md5s between Perl and C by bart
in thread Exchanging md5s between Perl and C by damian45

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