We are experiencing this same issue after upgrading to 12.1 RU6. Occuring on Windows 7 machines, both physical and virtual. Have been working with Symantec support for over a month. Haven't found a resolution yet.
Machines will shutdown/restart normally until the SEP client gets new A/V definitions. The SEP client tries to update the A/V engines with the new definitions, but not all of the engine parts get updated properly. After this, if you do a shutdown/restart the machine will get stuck on the Shutting Down screen, and you have to perform a hard shutdown. After you boot the machine up, the A/V engines will get updates, and you are able to shutdown/restart without issue. That is until your SEP client gets new definitions, which starts the problem over again.
Collected multiple sets of logs for Support, and they can't find an issue. Tried clean wipe and reinstall, same issue occurres. Tried many different combinations of client settings (PTP on and off, NTP on and off), only one that works is if you uninstall the A/V component and then the client is worthless.