Trying to Deploy either a .cmd or .bat file to update a registry Entry but not working

Hello.
I'm trying to deploy either a .cmd or .bat file to a few computers to update the registry and When I run the .cmd or .bat on the pc manually it works just fine. However when I create an application and try to deploy to the computers I keep getting the error
"The application was not detected after installation completed."
When I login to that computer I can tell that the file has not been run as none of the reg settings are changed
In the application properties I have tried cmd.exe "RegUpdate.cmd" and regedit /s "RegUpdate.cmd" and same result. Any ideas?

I have an application that has some different options for its configuration which all populate the registry.  The application has a option that when you set all the options like you want them you can click save as and it creates the .cmd file for you
with all the registry settings.
.cmd contents below:
@echo off
set SYSOPTS=%TEMP%\SysOpts.reg
set REGSWROOT=SOFTWARE
if [%PROCESSOR_ARCHITECTURE%]==[AMD64] set REGSWROOT=SOFTWARE\Wow6432Node
echo REGEDIT4 > %SYSOPTS%
echo. >> %SYSOPTS%
echo [HKEY_LOCAL_MACHINE\%REGSWROOT%\GeoGraphix\Tools\ProjectManager] >> %SYSOPTS%
echo @="List service communication parameters" >> %SYSOPTS%
echo "AllowIn"=dword:00000000 >> %SYSOPTS%
echo "SeeOut"=dword:00000001 >> %SYSOPTS%
echo "Concurrent"=dword:00000000 >> %SYSOPTS%
echo "ServiceStopType"=dword:00000002 >> %SYSOPTS%
echo "Protocol"=dword:00000002 >> %SYSOPTS%
echo "AllowNotifyReceive"=dword:00000000 >> %SYSOPTS%
echo "BroadcastType"=dword:00000002 >> %SYSOPTS%
echo "BroadcastAddr2"=hex(7):74,75,6c,67,67,78,2e,53,54,4d,2e,41,44,00,74,75,6c,67,67,78,32,2e,53,54,4d,2e,41,44,00,74,75,6c,67,67,78,33,2e,53,54,4d,2e,41,44,00,00, >> %SYSOPTS%
echo. >> %SYSOPTS%
echo [HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\SQLANYs_GGX\Parameters] >> %SYSOPTS%
echo "Parameters"="-n GGX_%COMPUTERNAME% -x TCPIP -xs HTTP(PORT=13386) -ti 0 -ch 15p -gd ALL -gp 8192" >> %SYSOPTS%
echo "ClientParameters"="-x TCPIP(IP=#SERVER_ADDRESS#;PORT=#SERVER_PORT#)" >> %SYSOPTS%
echo. >> %SYSOPTS%
echo [HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\GGX List Service (v2)] >> %SYSOPTS%
echo "Start"=dword:00000003 >> %SYSOPTS%
echo. >> %SYSOPTS%
echo [HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\GGX Network Access Service] >> %SYSOPTS%
echo "Start"=dword:00000003 >> %SYSOPTS%
echo. >> %SYSOPTS%
echo [HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\SQLANYs_GGX] >> %SYSOPTS%
echo "Start"=dword:00000003 >> %SYSOPTS%
%windir%\regedit.exe /s %SYSOPTS%
del /f %SYSOPTS%
set SYSOPTS=

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