The message says that the files do not appear to be from the same release as the rest of the install. Since you re-uploaded them, these messages would be expected.
Given your statement I would guess that mod_rewrite does not work on your server. If you will set mod_rewrite, remove the .htaccess file and then run setup again having it create the .htaccess file you should get an entry in the setup log with respect to htaccess. My guess is it will tell you that it does not work on your server.