The issue is caused by a missing variable on the 2012 R2 Server that was created during the agent installation.
To resolve this either install SP3 or follow this procedure:
Run the following line on the server and create the variable needed.
SET LDMS_LOCAL_DIR=C:\Program Files (x86)\LANDesk\LDClient\Data
Once complete ran a full sync scan with the following command line:
"C:\program files(x86)\LANDesk\LDClient\LDISCN32.EXE" /NTT=(name of core):5007 /S=(name of core) /I=HTTP://(nameofcore)/ldlogon/ldappl3.ldz /V /SYNC /F
After this has finished redeploy the PXE representative and this will resolve your issue.