For those who hit their heads about it, my experience shows that the error is erroneous or, at best, very misleading.
After viewing all the permissions, dragging and dropping the files from the Application Loader testing suite, the error magically disappeared, and the same files with the same permissions stopped giving the same error.
This is really not a solution, but it may be important to know that this error may not be what it seems (checked in 10.9.4).
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