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Now that’s odd. I just looked into the code at http://hg.python.org/cpython/file/2.7/Lib/shutil.py#l103 and there is a guard against EOPNOTSUPP:
try:
 os.chflags(dst, st.st_flags)
except OSError, why:
 if (not hasattr(errno, 'EOPNOTSUPP') or
 why.errno != errno.EOPNOTSUPP):
 raise
Does your /Library/Gentoo/usr/lib/python2.7/shutil.py look the same? Would you mind adding a `print why.errno` just before the raise?
I have tried move'ing files to NTFS and FAT32 and it works just fine here.