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Does Cygwin setup modify dlls?

In our project we like the Cygwin-Setup tool so much that we use it for our own files too.
Adding our archives to our setup.ini was easy enough and almost everything worked as expected.
But then a certain tool didn't work and we found that dll-files that were unpacked by the Cygwin-installer didn't match the files in the archive.
The problem seems to be dll-specific. Other filetypes are not modified.
When unpacking using normal Cygwin-tools (tar xf ...) all files were correct. So somehow the installation via Cygwin modifies them.
Is this known behaviour? Is this intentional? Can it be turned off? (Is there some postprocessing like "strip" etc?)
Or do you think we have another kind of problem, that is not related to Cygwin?
Our Cygwin-setup-version is 2.877, x86_64, running on Windows 10 or Windows 7.
Best regards,

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