Not sure if there is anything different about that particular Mac but you could just add

touch /private/etc/ntp.conf

To the start of the script to make sure it's there.

Try this:

#!/bin/sh

# Use "/usr/sbin/systemsetup -listtimezones" to see a list of available list time zones.
TimeZone="America/New_York"
TimeServer1="internalserver.com"
TimeServer2="time.apple.com"

############# Pause for network services #############
/bin/sleep 10
#################################################

/usr/sbin/systemsetup -setusingnetworktime off 

#Set an initial time zone
/usr/sbin/systemsetup -settimezone $TimeZone

#Set specific time servers
/usr/sbin/systemsetup -setnetworktimeserver $TimeServer1
echo "server $TimeServer2" >> /etc/ntp.conf

# enable location services
/bin/launchctl unload /System/Library/LaunchDaemons/com.apple.locationd.plist
uuid=`/usr/sbin/system_profiler SPHardwareDataType | grep "Hardware UUID" | cut -c22-57`
/usr/bin/defaults write /var/db/locationd/Library/Preferences/ByHost/com.apple.locationd.$uuid LocationServicesEnabled -int 1
/usr/sbin/chown -R _locationd:_locationd /var/db/locationd
/bin/launchctl load /System/Library/LaunchDaemons/com.apple.locationd.plist

# set time zone automatically using current location 
/usr/bin/defaults write /Library/Preferences/com.apple.timezone.auto Active -bool true

/usr/sbin/systemsetup -setusingnetworktime on 

/usr/sbin/systemsetup -gettimezone
/usr/sbin/systemsetup -getnetworktimeserver

exit 0

Does Ntp.conf reflect what time server is set at? So would my Ntp.conf just say. Ntp.blobface.xxx ?

On the computers that have the script run correctly it is setting the time zone to my current location of Washington DC, which is correct and the time is correct

What is this echo line for?

set specific time servers

/usr/sbin/systemsetup -setnetworktimeserver $TimeServer1
echo "server $TimeServer2" >> /etc/ntp.conf

GaToRaid - on a computer or two I get the following information in the LOG after my policy runs that uses the script you provided. Have you seen this before? what does it mean? doesn't seem to harm anything anyways.

Script result: setUsingNetworkTime: Off
Set TimeZone: America/New_York
setNetworkTimeServer: ntp.blobface.xxx
2015-03-11 11:18:24.362 system_profiler[10090:226920] platformPluginDictionary: Can't get X86PlatformPlugin, return value 0
2015-03-11 11:18:24.364 system_profiler[10090:226920] platformPluginDictionary: Can't get X86PlatformPlugin, return value 0
setUsingNetworkTime: On
Time Zone: America/New_York
Network Time Server: ntp.blobface.xxx

@tcandela sorry for the delayed. Yes this error will be a problem since you are not enabling location services. Which OS are you running this on?

Isn't the script enabling location services ? i see the check box checked in the 'privacy' section to enable location services. what problem is the log telling ?

these computers are mostly ethernet connected, in the TIME ZONE TABE it says 'turn on wifi to determine your current location'

I am running this on 10.7 10.8 10.9 10.10

so far on 32 computers that the script ran on, 3 computers got this message in the log

1 - MBAir 13" mid 2011 10.10.2
2 - iMac early 2009 10.10.2
3 - iMac (21.5-inch, Mid 2011) 10.10.1

also, on some computer after the policy with this script runs etc/ntp.conf lists both ntp servers server ntp.blobface.xxx
server time.apple.com
while on others it lists just
server ntp.blobface.xxx

and the system preferences date & Time has both time servers in the text box ntp.blobface.xxx, time.apple.com
while on others it lists just ntp.blobface.xxx

@tcandela ah you are right regarding the location services, we do turn that on with this script(sorry been at a conference for the last week, my head is a bit of mush.)

As for the issue that you are seeing is something to do with system profiler. Try running the command manually without the grep in it(i.e. /usr/sbin/system_profiler SPHardwareDataType) and see if you are able to return something.

And regarding the servers not getting listed, I would try and manually run the script one line at a time and see what results. I haven't had this issue before.

From the command line What I get when running the /user/sbin/sysyem_profiler SPHardwareDataTpe is the same message as above, plus hardware overview information.

When I run it from the CL with Grep in it , I get the same two lines, plus a third line displaying the Hardware UUID

What is this line supposed to do?
Seems to be happening only on yosemite

From CL When I run sudo server Ntp.blobface.xxx >> /etc/ Ntp.conf ( with or without sudo)
I get. -bash: /etc/Ntp.conf: permission denied

This is from 10.10.2. System

should be something more like

sudo sh -c "echo ntp.blobface.xxx >> /etc/ntp.conf"

nessts - I ran the command your provided from the CL on a computer that did not get both servers added to the ntp.conf file, and it worked

sudo sh -c "echo server ntp.blobface.xxx >> /etc/ntp.conf"

should i revamp the script section to what you see below?
CASPER doesn't need sudo so leave it out ? also the quotes go from "server ..... .conf" ?

Set specific time servers

/usr/sbin/systemsetup -setnetworktimeserver $TimeServer1
sh -c echo "server $TimeServer2 >> /etc/ntp.conf"

well it all depends how and what you are trying to do. running it from the command line is wholly different than doing it in a casper policy,
you do not need the sudo sh -c and the 2 "
I was just helping you fix your command line issue.
you don't even have to use sysetemsetup to do the first one if you don't want to. The script looked to be correct as it was.

trying to figure out why this line works on some computers and not others

echo "server $TimeServer2" >> /etc/ntp.conf

@tcandela A better way to set time servers, time zone, etc:

systemsetup -settimezone America/Chicago

# enable network time
systemsetup -setusingnetworktime on

# set the time server
timeServer='time.apple.com'
systemsetup -setnetworktimeserver $timeServer

That's the method I use, and I haven't had a problem using that method since 10.6.

I realized that you were trying to set two time servers. According to this discussion on JAMF Nation:

Best way to set multiple NTP servers in 10.7.x and 10.8.x?

You can use systemsetup and just put a comma between the servers:

systemsetup -setnetworktimeserver $timeServer1,$timeServer2

Ah, right you are @nessts! I simply found that info in that discussion, and didn't verify the info was correct. Thanks for correcting me Todd!

that is what I am here for trying to bring a little Unix sense to a Mac world. :)