Problem with script based site creation

I created a simple bash script that would create the folder structues and more imporatnatly, the http-conf files for the given sites. However, while the script works... and all seems well... in short time, the server will place all conf files into a "sites-previous-unusable" folder.
Here is the other confusing part. Everything was working late last week, but when I got back to the servers from a long weekend... server.app could not tell that apache was running. After a few re-openings of server.app, eventually it starting failing on being able to read the server config.
If anyone could help... please... any input or suggestions would be greatly appreciated.
Recap of issues we are seeing:
Apache begins to ignore all virtuals, and routes all to the default directory (/var/empty)
All conf files get moved to a "sites-previous-unusable" directory in /etc/apache2
What we are trying to do...
We are trying to automate the process of creating folder and domain/subdomain structures for the design and development of our client sites. (see below script). Being that we have hundredes of sites... so an automated process is very much needed as server.app is a horrible interface for anything more then 5.
-Michael
#! /bin/bash
# =======================
# Siteup Script 1.0
# Released:
# =======================
# =======================
# The Script can only be run
# under root level privileges
# =======================
ROOT_UID=0     # Only users with $UID 0 have root privileges.
E_NOTROOT=67   # Non-root exit error.
if [ "$UID" -ne "$ROOT_UID" ]
then
  echo "Must be root to run this script."
  exit $E_NOTROOT
fi
# =======================
#          set functions
# =======================
# =======================
# functions: make_vhost
# Description:
# =======================
function make_index
cat <<- _EOF_
          <!doctype html>
          <html>
                    <head>
                              <title>PLaceholder For: $DNAME</title>
                              <meta charset="utf-8" />
                    </head>
                    <body>
                    <header>
                              <h1>Placeholder</h1>
                    </header>
                    <content>
                              <div>Client Domain: $DNAME</div>
                              <div>File Location: $ROOTDIR/$FPATH</div>
                    </content>
                    <footer>
                              <div>Copyleft 2010 - Our Company</div>
                    </footer>
                    </body>
          </html>
_EOF_
# =======================
# functions: make_vhost
# Description:
# =======================
function make_vhost {
cat <<- _EOF_
<VirtualHost 192.168.23.13:80>
          ServerAdmin [email protected]
          ServerName $SITE
          Alias /apache-resources "/etc/apache2/resources"
          DirectoryIndex index.html index.htm index.php
          DocumentRoot $PNAME/$FNAME/$DNAME/$FPATH
          <Directory $PNAME/$FNAME/$DNAME/$FPATH>
                    AllowOverride All
                    Order allow,deny
                    Allow from all
                    # Tell Apache to add theme support to autoindex
                    <IfModule mod_autoindex.c>
                              Options Indexes FollowSymLinks MultiViews
                              IndexOptions +FancyIndexing
                              IndexOptions +VersionSort
                              IndexOptions +HTMLTable
                              IndexOptions +FoldersFirst
                              IndexOptions +IconsAreLinks
                              IndexOptions +IgnoreCase
                              IndexOptions +SuppressRules
                              IndexOptions +SuppressDescription
                              IndexOptions +SuppressHTMLPreamble
                              IndexOptions +XHTML
                              IndexOptions +IconWidth=16
                              IndexOptions +IconHeight=16
                              IndexOptions +NameWidth=*
                              IndexOrderDefault Descending Name
                              IndexStyleSheet /apache-resources/css/autoindex.css
                              HeaderName /apache-resources/include/header.html
                              ReadmeName /apache-resources/include/footer.html
                              IndexIgnore .??* *~ *# HEADER* README* RCS CVS *,v *,t
                    </ifModule>
          </Directory>
          ErrorLog          $PLOGS/$FNAME/$DNAME/error_log
          CustomLog          $PLOGS/$FNAME/$DNAME/access_log combined
</VirtualHost>
_EOF_
# =======================
#               header
# =======================
clear
# =======================
# set domain name variable
# =======================
# echo "==> Enter new domain name (domain.com): " ; read FQDN
read -p "==> Enter new domain name (domain.com): " FQDN
# =======================
# set support variables
# =======================
HOSTNAME=`echo $FQDN |awk -F. '{ print $1 }'`
DOMAIN=`echo $FQDN |awk -F. '{$1="";OFS="." ; print $0}' | sed 's/^.//' `
DNAME=$FQDN
FNAME=`echo ${FQDN:0:1} | tr 'a-zA-Z' 'A-Za-z'`
PNAME="/Users/Shared/ClientDomains"
PLOGS="/var/log/apache2"
ROOTDIR="$PNAME/$FNAME/$DNAME"
# =======================
# create needed directories
# =======================
mkdir -vp $ROOTDIR/archive && chmod 0777 $ROOTDIR/archive
mkdir -vp $ROOTDIR/digital-assets
mkdir -vp $ROOTDIR/digital-assets/design && chmod 0777 $ROOTDIR/digital-assets/design
mkdir -vp $ROOTDIR/digital-assets/images && chmod 0777 $ROOTDIR/digital-assets/images
mkdir -vp $ROOTDIR/instances
mkdir -vp $ROOTDIR/staging
mkdir -vp $ROOTDIR/production
mkdir -vp $ROOTDIR/templates
mkdir -vp $ROOTDIR/subdomains
mkdir -vp $ROOTDIR/subdomains/emailers
mkdir -vp $ROOTDIR/subdomains/landingpages
mkdir -vp $ROOTDIR/subdomains/sweepstakes
mkdir -vp $PLOGS/$FNAME/$DNAME
touch $PLOGS/$FNAME/$DNAME/access_log
touch $PLOGS/$FNAME/$DNAME/error_log
SDOMAIN=( "production" "staging" "templates" "emailers" "landing" "sweepstakes" )
SPATHS=( "production" "staging" "templates" "subdomains/emailers" "subdomains/landingpages" "subdomains/sweepstakes" )
ASIZE=${#SDOMAIN}
for ((i=0;i<$ASIZE;i++)); do
          if [ -z ${SDOMAIN[${i}]} ]
          then
                    continue
          else
                    SITE="${SDOMAIN[${i}]}.$HOSTNAME.ourcompany.com"
                    FPATH=${SPATHS[${i}]}
                    # =======================
                    # build index.html file
                    # =======================
                    # We actually only want this for the first 3
                    if [ $i -lt "3" ]
                    then
                              make_index > "$ROOTDIR/$FPATH/index.html"
                    fi
                    # =======================
                    # build vhost config file
                    # =======================
                    ACONF="0000_192.168.23.13_80_$SITE.conf"
                    make_vhost > /etc/apache2/sites/$ACONF
          fi
done
# =======================
#    exit
# =======================
apachectl restart
exit

I was just doing the same thing.  Although I realize this post is getting old.
I did it by using:
strRegEnv   = "HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Session Manager\Environment\SAPLOGON_INI_FILE"
NwEngine.Shell.SetRegValue strRegEnv, "REG_SZ", "(FILE LOCATION)"
I placed that at the "On end Install" and "On end Update" Level.
if the reg value is not already present, it will be created.
If the reg value does exist, it is replaced.
Hope that helps.

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        + CategoryInfo          : NotSpecified: (:) [], MethodInvocationException
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    http://technet.microsoft.com/en-us/library/ff730951.aspx but these solutions also failed to have any effect.
    My second problem is when I try to apply the newly-created security groups, I also will get the "Some or all identity references could not be translated."  I thought I had found a workaround to the problem by adding the -PassThru option to
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    Thanks!

    I was hoping to stay with strictly Powershell, but unless I can find a Powershell solution, I may resort to ICACLS.
    As for the problems with my groups not being translatable right after creating them, I think I have solved this problem by using the -Server parameter on all my New-ADGroup commands and this example code seems to have gotten around the translation problem,
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