I found that OSSEC opens the files in text mode, and this seems to produce 
wrong hashes. Files should be opened in binary mode to work properly.

I fixed this problem in our repository: 
https://github.com/wazuh/ossec-wazuh/commit/f52514647f0be8ae01a83c260bdad85d24eb8cd9

And I also sent a pull-request to OSSEC: 
https://github.com/ossec/ossec-hids/pull/744

I hope this solves the issue.
Best regards.

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