The list of binary files that differ:

================================================================================
Binary files iter1/sbin/mkfs and iter2/sbin/mkfs differ
Binary files iter1/usr/bin/bison and iter2/usr/bin/bison differ
Binary files iter1/usr/bin/perl and iter2/usr/bin/perl differ
Binary files iter1/usr/bin/perl5.8.7 and iter2/usr/bin/perl5.8.7 differ
Binary files iter1/usr/bin/vim and iter2/usr/bin/vim differ
Binary files iter1/usr/include/c++/4.0.2/i686-pc-linux-gnu/bits/stdc++.h.gch/O0g.gch and iter2/usr/include/c++/4.0.2/i686-pc-linux-gnu/bits/stdc++.h.gch/O0g.gch differ
Binary files iter1/usr/include/c++/4.0.2/i686-pc-linux-gnu/bits/stdc++.h.gch/O2g.gch and iter2/usr/include/c++/4.0.2/i686-pc-linux-gnu/bits/stdc++.h.gch/O2g.gch differ
Binary files iter1/usr/lib/libstdc++.a/bitmap_allocator.o and iter2/usr/lib/libstdc++.a/bitmap_allocator.o differ
Binary files iter1/usr/lib/libstdc++.a/guard.o and iter2/usr/lib/libstdc++.a/guard.o differ
Binary files iter1/usr/lib/libstdc++.a/locale-inst.o and iter2/usr/lib/libstdc++.a/locale-inst.o differ
Binary files iter1/usr/lib/libstdc++.a/vec.o and iter2/usr/lib/libstdc++.a/vec.o differ
Binary files iter1/usr/lib/libstdc++.a/wlocale-inst.o and iter2/usr/lib/libstdc++.a/wlocale-inst.o differ
Binary files iter1/usr/lib/libstdc++.so.6.0.6 and iter2/usr/lib/libstdc++.so.6.0.6 differ
Binary files iter1/usr/lib/libsupc++.a/guard.o and iter2/usr/lib/libsupc++.a/guard.o differ
Binary files iter1/usr/lib/libsupc++.a/vec.o and iter2/usr/lib/libsupc++.a/vec.o differ
Binary files iter1/usr/lib/locale/locale-archive and iter2/usr/lib/locale/locale-archive differ
Binary files iter1/usr/lib/perl5/5.8.7/i686-linux/CORE/libperl.a/perl.o and iter2/usr/lib/perl5/5.8.7/i686-linux/CORE/libperl.a/perl.o differ
Binary files iter1/usr/sbin/nscd and iter2/usr/sbin/nscd differ

The list of files that exist "only in" 1 of the directories:

================================================================================
Only in iter2/etc: gshadow-