Interesting about the boxed DVD version. Maybe this turns out to be affecting all steam versions, for example? It's not the first time steam and other versions have had quirks. The steam version already broke the setup executable (it is not possible to launch it and set up your hardware stuff before launching the game, everything must be done in game or in the conf.ini file).
Regarding your erronous edited thingy, it's nothing special
But useful to be left for clarification for others who might not be as sure. Don't let personal prestige affect you.
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To be specific, my steam version, first downloaded (and later redownloaded) was the one pre-patched to 4.08, which could make a difference, because they provide the whole folder, as if it was already installed from a DVD and patched to 4.08. Someone having a steam version which was pre-patched to an older version might have been able to avoid getting the same (possibly broken) files, as they patched to 4.08 and onwards manually.