Hi Ishaq,
Check the logs in detail (or examine the Windows Application Event Log entries). What action does SEP report was taken? I suspect that you will see "Partially Removed" or similar for some of those threats.
This KB has more information: What Does "Risk was partially removed" Mean? (http://www.symantec.com/docs/TECH94475)
A full system scan in safe mode will, under most circumstances, completely remove threats that were "partially removed" earlier. Be sure to check the risk log after the scan has been run for confirmation.
Hope this helps! Please keep this thread up-to-date with your progress.
Thanks and best regards,
Mick