Ok, got NTLM authentication to work.
Following changes were made:
web.xml
Switched to NTLMAuthenticationFilter
<filter>
<filter-name>Authentication Filter</filter-name>
<filter-class>org.alfresco.web.app.servlet.NTLMAuthenticationFilter</filter-class>
</filter>
<filter>
<filter-name>WebDAV Authentication Filter</filter-name>
<filter-class>org.alfresco.repo.webdav.auth.NTLMAuthenticationFilter</filter-class>
</filter>
Un-commented the following 3 mappings
<filter-mapping>
<filter-name>Authentication Filter</filter-name>
<url-pattern>/navigate/*</url-pattern>
</filter-mapping>
<filter-mapping>
<filter-name>Authentication Filter</filter-name>
<url-pattern>/command/*</url-pattern>
</filter-mapping>
<filter-mapping>
<filter-name>Authentication Filter</filter-name>
<url-pattern>/template/*</url-pattern>
</filter-mapping>
In \Alfresco\tomcat\shared\classes\alfresco\extension folder
rename ntlm-authentication-context.xml.sample to ntlm-authentication-context.xml
Replace the following with
<property name="useLocalServer">
<value>true</value>
</property>
with
<property name="domain">
<value>VALUE OF YOUR DOMAIN</value>
</property>