Ran into this also. Thanks to reinhold for pointing to the patch.

I am just using the stock Ubuntu 12.04 version with the patch manually
applied. That is working fine for me in terms of avoiding the false
positive.

vi /usr/bin/rkhunter

    At around line 846 and following

...
                        elif [ -d "${FNAME}" ]; then
                                #
                                # For the ALLOWHIDDENFILE option we need to 
allow
                                # a hidden symbolic link to a directory.
                                #
                                test "${OPT_NAME}" = "ALLOWHIDDENFILE" -a -h 
"${FNAME}" && continue

                                case "${OPT_NAME}" in
...

    At around line 15102 and following (the change is just a comment)

...
                FTYPE=`${FILE_CMD} ${FNAME} 2>/dev/null | cat -v | tr -s '      
 ' '  ' | cut -d' ' -f2-`
 
#jh - should include block special too.
#jh - also should cater for 'sticky directory' (like /tmp) when using file.
                test -z "${FTYPE}" -o -n "`echo \"${FTYPE}\" | egrep 'character 
special|empty'`" && continue
... 

Update the signature database as the rkhunter file signature has changed
with the edits above.

rkhunter --propupd


And here are the other configuration settings I needed to add to avoid false 
positives on Ubuntu 12.04 Server.

vi /etc/rkhunter.conf

Avoid hidden directory/hidden file false positives

...

#
# Allow the specified hidden directories to be whitelisted.
#
# This is a space-separated list of directory pathnames.
# The option may be specified more than once. The option
# may use wildcard characters.
#
#ALLOWHIDDENDIR="/etc/.java"
#ALLOWHIDDENDIR="/dev/.static"
#ALLOWHIDDENDIR="/dev/.initramfs"
#ALLOWHIDDENDIR="/dev/.SRC-unix"
#ALLOWHIDDENDIR="/dev/.mdadm"
## add /dev/.udev directory to avoid a false positive
ALLOWHIDDENDIR="/dev/.udev

#
# Allow the specified hidden files to be whitelisted.
#
# This is a space-separated list of filenames. The option may
# be specified more than once. The option may use wildcard
# characters.
#
#ALLOWHIDDENFILE="/etc/.java"
...
#ALLOWHIDDENFILE="/usr/share/man/man5/.k5login.5.gz"
## add /dev/.initramfs symbolic link to avoid a false positive
ALLOWHIDDENFILE="/dev/.initramfs"

...

Avoid "replaced by a script" false positives

...

#
# Allow the specified commands to be scripts.
#
# This is a space-separated list of filenames. The option may
# be specified more than once. The option may use wildcard
# characters.
#
SCRIPTWHITELIST=/bin/egrep
SCRIPTWHITELIST=/bin/fgrep
SCRIPTWHITELIST=/bin/which
SCRIPTWHITELIST=/usr/bin/groups
SCRIPTWHITELIST=/usr/bin/ldd
SCRIPTWHITELIST=/usr/bin/lwp-request
SCRIPTWHITELIST=/usr/sbin/adduser
SCRIPTWHITELIST=/usr/sbin/prelink
## add /usr/bin/unhide.rb to avoid a false positive
SCRIPTWHITELIST=/usr/bin/unhide.rb

...

Regards,
Tim Miller Dyck

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https://bugs.launchpad.net/bugs/883324

Title:
  False positive: Hidden file (symbolic link to directory) cannot be
  white-listed

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