Have a look at the logs on the core...find the log with the CJ-OSD XXXXXXX, it should give you an idea where it failed..
One reason--CTOS is where most fail, ours failed on it due to the SQL database the driver database was handing the driver files with the slashes "/" the wrong way, I had to use SQLite and edit the database.3db every time we added or saved the new drivers..(only effects SP3). CTOS should reboot the machine and then continue with the script from the core, if any drivers fail-CTOS fails..hence the following system configuration not completeing.
Another reason-- I put in a wait just after the agent of 120 seconds, it then continues to install my other applications-just before reboot I stick in another wait, this time 180, so that any applications can finish off, this is for Sophos to update itself/complete..
hope this helps.