Some applications may have specific mitigations disabled in the Application Configuration policy in Enhanced Mitigation Experience Toolkit (EMET). These disabled mitigations may not take effect when one or both of the following EMET policies are also enabled:
Default Protections for Popular Software
Default Protections for Recommended Software
EMET policies are not cumulative. When Default Protections policies are applied in addition to the Application Configuration policy, duplicate entries for the same application may occur, and you cannot prioritize the Application Configuration settings. For example, because the Default Protections for Popular Software policy enables all mitigations for a set of applications, any of the same applications that are configured through the Application Configuration policy with mitigations disabled will not take effect.
To resolve this issue, do not enable the Default Protections policy settings. Instead, enable only the Application Configuration policy, and create individual entries for each application that has to have some or all mitigations enabled or disabled.