Which character set do you have? I notice that the files in question are binary (non-text), and I know some of our Chinese friends have had problems when using the installer on their character set, perhaps some others also cause problems. In their case, manually extracting with 7-zip seems to work, so you could try that.
The files under ./data that are "changed" are not from the EB installer. You should be able to restore those by installing a clean 1.5 RTW.
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