atlas3.10.1.tar.bz2 contains multiple reference to same files. It makes some extraction utilities confused. Current version of archive for example stops one from updating atlas package for Arch Linux. See http://code.google.com/p/libarchive/issues/detail?id=299 for discussion about this issue on libarchive tracker, one of software that cannot extract archives with multiple files with same name. Fixing this would be as simple as repackaging the archive with correct options.
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