When running the Differences Report, differences are detected between GPOs with the same name located in different domains. However, upon reviewing the generated HTML report, no differences are displayed, despite the report indicating that discrepancies were found.
The Differences report is not reporting any incorrect results. The differences shown are based on the contents of the backup files being compared.
Although the settings appear identical in the report, the corresponding entries in the backup.xml files contain different UID values. As a result, they are treated as different settings and are correctly reported as such. While this can be confusing when viewing the readable report output, the underlying data indicates that the settings are technically different.