I have made some of the suggested changes to the adlogon.cmd

 Code:
...
set HERE=%~dp0
...
set RUNDIR=%TEMP%\ADLogon
...
:: KIX drive mappings
  echo Starting AD logon script for %USERDNSDOMAIN%...
  echo Copying KIX32/KIX Script/Mapping file to %TEMP%\ADLogon...

  :: Copy to local machine to prevent running from DC (AV issues etc)
  xcopy %HERE%* %RUNDIR%\ /Y /E /C

  echo  %RUNDIR%\kix32.exe "%RUNDIR%\adlogon.kix" $adlcdir="%RUNDIR%" "$logfile=%KIXLOG%"
  %RUNDIR%\kix32.exe "%RUNDIR%\adlogon.kix" $adlcdir="%RUNDIR%" "$logfile=%KIXLOG%"


I've emailed this script to a domain administrator that I've been working with on this issue. Now to wait and see what he comes back with.

Thank you everyone so far.