in reply to Re: Exchanging md5s between Perl and C
in thread Exchanging md5s between Perl and C

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');
Result:
0cc175b9c0f1b6a831c399e269772661 *tempfile
So yeah, md5sum and Digest::MD5 agree.

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

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Re^3: Exchanging md5s between Perl and C
by damian45 (Novice) on Oct 28, 2010 at 19:54 UTC

    ahhk! thank you very much, yes that was it.

    I previously had an issue with 32/64 bit and after going round and round until fixed, somewhere along the line I stared chasing my tail overlooking that minor but oh so important detail.

    cheers for you time! Glad it was as simple as that