rndc.conf.sample is not installed by the port, but it is isted in pkg-plist:

# grep rndc.conf.sample /usr/ports/dns/bind99/pkg-plist 
%%BIND_DESTETC%%/rndc.conf.sample


--->  Backing up the old version
--->  Uninstalling the old version
--->  Deinstalling 'bind99-9.9.5_16'
[Updating the pkgdb <format:bdb_btree> in /var/db/pkg ... - 60 packages found (-1 +0) (...) done]
--->  Installing the new version via the port
===>  Building package for bind99-9.9.5_17
Creating package /usr/ports/dns/bind99/work/pkg/bind99-9.9.5_17.tbz
Registering depends: idnkit-1.0_3 libxml2-2.9.1_1 libiconv-1.14_3 openssl-1.0.1_13.
Registering conflicts: bind9*-9.[45678].* bind9*-sdb-9.[45678].* bind-tools-9.* bind-tools-9.*.
Creating bzip'd tar ball in '/usr/ports/dns/bind99/work/pkg/bind99-9.9.5_17.tbz'
tar: /usr/local/etc/rndc.conf.sample: Cannot stat: No such file or directory
tar: Error exit delayed from previous errors.
pkg_create: make_dist: tar command failed with code 256
*** [do-package] Error code 1

Stop in /usr/ports/dns/bind99.
*** [install] Error code 1

Stop in /usr/ports/dns/bind99.
*** [reinstall] Error code 1

Stop in /usr/ports/dns/bind99.
** Command failed [exit code 1]: /usr/bin/script -qa /tmp/portupgrade20140607-21614-evh5xl env UPGRADE_TOOL=portupgrade UPGRADE_PORT=bind99-9.9.5_16 UPGRADE_PORT_VER=9.9.5_16 make DEPENDS_TARGET=package -DFORCE_PKG_REGISTER reinstall
--->  Restoring the old version
pkg_install EOL is scheduled for 2014-09-01. Please consider migrating to pkgng
http://blogs.freebsdish.org/portmgr/2014/02/03/time-to-bid-farewell-to-the-old-pkg_-tools/

*************************************************************************
*           _  _____ _____ _____ _   _ _____ ___ ___  _   _             *
*          / \|_   _|_   _| ____| \ | |_   _|_ _/ _ \| \ | |            *
*         / _ \ | |   | | |  _| |  \| | | |  | | | | |  \| |            *
*        / ___ \| |   | | | |___| |\  | | |  | | |_| | |\  |            *
*       /_/   \_\_|   |_| |_____|_| \_| |_| |___\___/|_| \_|            *
*                                                                       *
*       If you are running BIND 9 in a chroot environment, make         *
*       sure that there is a /dev/random device in the chroot.          *
*                                                                       *
*       BIND 9 also requires configuration of rndc, including a         *
*       "secret" key.  The easiest, and most secure way to configure    *
*       rndc is to run 'rndc-confgen -a' to generate the proper conf    *
*       file, with a new random key, and appropriate file permissions.  *
*                                                                       *
*       The /etc/rc.d/named script in the base will do both for you.    *
*                                                                       *
*************************************************************************

** Fix the installation problem and try again.
[Updating the pkgdb <format:bdb_btree> in /var/db/pkg ... - 61 packages found (-0 +1) . done]
** Listing the failed packages (-:ignored / *:skipped / !:failed)
        ! dns/bind99 (bind99-9.9.5_16)  (install error)
Update failed