ntpdate complains about missing libmd5.so, which is contained in the the libwww package. ntp is in [extra] and libwww is in [community], so the latter should be moved. This only affects x86_64, because (strangely enough) ldd shows quite a difference on i686.

i686:
$ ldd /usr/bin/ntpdate
linux-gate.so.1 => (0xb8028000)
libc.so.6 => /lib/libc.so.6 (0xb7eb2000)
/lib/ld-linux.so.2 (0xb8029000)

x86_64:
$ ldd /usr/bin/ntpdate
linux-vdso.so.1 => (0x00007fff4a7fe000)
libmd5.so.0 => /usr/lib/libmd5.so.0 (0x00007f4642376000)
libc.so.6 => /lib/libc.so.6 (0x00007f4642022000)
libdl.so.2 => /lib/libdl.so.2 (0x00007f4641e1e000)
libz.so.1 => /usr/lib/libz.so.1 (0x00007f4641c09000)
libssl.so.0.9.8 => /usr/lib/libssl.so.0.9.8 (0x00007f46419b9000)
libcrypto.so.0.9.8 => /usr/lib/libcrypto.so.0.9.8 (0x00007f464162a000)
/lib/ld-linux-x86-64.so.2 (0x00007f4642578000)

Is this intentional? There are also some linking differences in the ntpd binaries:

i686:
$ ldd /usr/bin/ntpd
linux-gate.so.1 => (0xb7ef4000)
libm.so.6 => /lib/libm.so.6 (0xb7e9f000)
libcrypto.so.0.9.8 => /usr/lib/libcrypto.so.0.9.8 (0xb7d49000)
libc.so.6 => /lib/libc.so.6 (0xb7c02000)
/lib/ld-linux.so.2 (0xb7ef5000)
libdl.so.2 => /lib/libdl.so.2 (0xb7bfe000)
libz.so.1 => /usr/lib/libz.so.1 (0xb7bea000)

x86_64:
$ ldd /usr/bin/ntpd
linux-vdso.so.1 => (0x00007fff1c9fe000)
libm.so.6 => /lib/libm.so.6 (0x00007fa81440b000)
libcrypto.so.0.9.8 => /usr/lib/libcrypto.so.0.9.8 (0x00007fa81407c000)
libmd5.so.0 => /usr/lib/libmd5.so.0 (0x00007fa813e7a000)
libc.so.6 => /lib/libc.so.6 (0x00007fa813b26000)
libdl.so.2 => /lib/libdl.so.2 (0x00007fa813922000)
libz.so.1 => /usr/lib/libz.so.1 (0x00007fa81370d000)
libssl.so.0.9.8 => /usr/lib/libssl.so.0.9.8 (0x00007fa8134bd000)
/lib/ld-linux-x86-64.so.2 (0x00007fa81468e000)