I've been getting lots of complaints about this kind of thing here too.
I updated our MR2 clients with no Network Threat Protection switched on to 11.0.4014.26 with Network Threat Protection on earlier this year and started getting lots of complaints about slow logins, machines hanging, documents not opening quickly from servers. I put it down to the version of SEP and updated to RU5 but nothing changed.
Uninstalling the Network Threat Protection part of things seems to be fixing a lot of the issues.
The probem is one of the reasons we bought SEP was for Application and Device control which you can't do unless you've got Network Threat Protection installed and enabled. Having a hard time explaining to the boss that all that money we spent on SEP looks to be wasted as we can't use the functionality we want!