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A default of the programs you use perhaps... if I upload a file with ftp (using ftp server mod) it does not have +x flags. But that depends on the FTP client as well.
If you make your own KoboRoot.tgz without having the means of unbricking, you better double- and triplecheck the resulting tar file before actually putting it on the reader. I've mentioned this before but the Kobo itself does very little in the way of sanity checking. It does not verify that the tar file is intact, nor that the files inside have proper permissions set.
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