I think that copying the security settings for the files is taking a long time. Maybe you should make sure that the scheduler is running under the same user account under which you say that manual runs work fine. So if you have installed it as a service, you may want to change the service account.
Please send a log file for a manual run and one for the run causing SPCSX to me so I can compare it.
SPCSX is not an error, it just means that something is taking longer than 1 minute. Maybe if you are working with Virtual Machines or other machines that don't perform well, such as NAS devices, then you may have to live with it.