This seems like a bug:
When copying files from a ZIP/RAR archive from within MC to a folder which already contains those files, and the files are readonly, then the copy will fail. You don't get the option to overwrite readonly files (which you do when copying files from a normal folder), nor do you get a warning that there were problems copying.
This is an annoying bug. It causes a lot of confusion when folders are only partially updated (or not at all) without any notification of a problem.
