Downstream report you should read,
http://bugs.gentoo.org/show_bug.cgi?id=511634

Basically Makefile's are always including src/x86/win32.S even on a
non-windows system, and win32.S is missing the GNU stack
marking other files already have:

Makefile.am has:

if X86
nodist_libffi_la_SOURCES += src/x86/ffi.c src/x86/sysv.S src/x86/win32.S
endif

and it doesn't have the

#if defined __ELF__ && defined __linux__
    .section        .note.GNU-stack,"",@progbits
#endif

other files like sysv.S, unix64.S, freebsd.S, already have

The attached patch fixes the executable stack in libffi.so.6