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When you generate a Snapshot Comparison, the report may indicate that differences exist in the file, folder, or registry key permissions when, in fact, there are no differences. This issue is most likely to occur when Windows user accounts have been granted multiple permissions on those files, folders, or registry keys.

Assessment Comparison server list reflects policy membership only

When you generate an Assessment Comparison, the SQL Server report parameter lists the instances that are currently audited by the original policy. This behavior can create unexpected report results when the assessments you are comparing audit different instances from those included in the original policy. To view all available audit data, select All servers in policy for the SQL Server report parameter.