Hello,
Was there Network Threat Protection installed in SEP 11.x before?
I wonder since the Network Threat Protection was previously installed and now it isn't installed in SEP 12.1, the Windows Firewall might have got enabled.
About Windows Firewall and Symantec Endpoint Protection's NTP
http://www.symantec.com/docs/TECH97986
Advanced Settings for Windows 7 Firewall indicate that it is on, even when Symantec Endpoint Protection (SEP) Network Threat Protection (NTP) is installed.
http://www.symantec.com/docs/TECH123729
How to keep Windows 2008 Small Business Server firewall from showing critical when SEP's Network Threat Protection is enabled
http://www.symantec.com/docs/TECH95700
Hope that helps!!