Hello,
By default, scheduled scan peformance options (in Scan Options, Advanced) are set to "Best Application Peformance". When you configure a scan with this setting, scans will start but they only run when the client computer is idle. You can change this for faster scan performance, but user applications may run slower while the scan runs.
In Scan Schedule options, you may choose "Scan for up to N hours". If the scan has not completed by that time, it will resume at the next scheduled time or at a randomized time within that interval. The default scheduled scan that comes with Symantec Endpoint Protection is set to scan up to 2 hours and to resume at a random point in that time. Choose "Scan until finished" to run the scan without interruption.
"Missed Scheduled Scans", also under Scan Schedule options, may start a scan at an unexpected time. This option will retry a scan within the specified interval if the computer is off or unable to start the scan at the specified time. Uncheck this box to start the scan only at the scheduled time.
Check this Article:
SEP 12.1 and Advance Scanning
https://www-secure.symantec.com/connect/articles/sep-121-and-advance-scanning
Configuring SEP client options for end users to stop, pause, or 'snooze' administrator defined scans
http://www.symantec.com/docs/TECH93376
Can Symantec Endpoint Protection clients be configured to pause all scan types except for Administrator defined scans?
http://www.symantec.com/docs/TECH105383
Hope that helps!!