Unforeseen Consequences: How September’s Windows Server Updates Impacted Active Directory

Windows Server 2025 Security Update Causes Active Directory Issues

Microsoft has acknowledged that the security updates released in September 2025 are leading to Active Directory problems on Windows Server 2025 systems.

According to a recent update on the Windows release health dashboard, this issue specifically impacts Active Directory Domain Services (AD DS) synchronization, including Microsoft Entra Connect Sync.

The tech giant explained, “Applications utilizing the Active Directory directory synchronization (DirSync) control for on-premises Active Directory Domain Services (AD DS), such as with Microsoft Entra Connect Sync, may experience incomplete synchronization of large AD security groups with over 10,000 members.”

This issue is isolated to Windows Server 2025 post the installation of the September 2025 Windows security update (KB5065426) or subsequent updates.

Microsoft’s engineering teams are actively working on resolving these AD sync challenges and have shared a temporary workaround until a permanent fix is available.

IT administrators are advised to promptly add the following registry key to prevent disruptions in Microsoft Entra Connect Sync:

    Path: Computer\HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Policies\Microsoft\FeatureManagement\Overrides

    Name: 2362988687

    Type: REG_DWORD

    Value: 0

However, Microsoft cautioned that incorrect modifications to the registry using Registry Editor or any other method could lead to severe issues that might necessitate operating system reinstallation.

The company emphasized that it cannot guarantee the resolution of such problems and that administrators modify the registry at their own risk.

Although the root cause of these synchronization issues was not disclosed, a support document outlining the current prerequisites for Microsoft Entra Cloud Sync mentioned that “Windows Server 2025 support for Microsoft Entra Cloud Sync is anticipated in a future release.”

Additional Windows Server 2025 Issues

Microsoft is also addressing another known issue affecting Windows 11 24H2 and Windows Server 2025 devices, resulting in Windows update failures when installing updates from a network share using the Windows Update Standalone Installer (WUSA).

While a comprehensive fix for this issue is pending, Microsoft is automatically mitigating it on home and non-managed business devices through Known Issue Rollback (KIR).

In a recent emergency update in July, Microsoft resolved a bug that was preventing Azure VMs from launching when Virtualization-Based Security (VBS) was enabled and the Trusted Launch setting was disabled.

Prior to that, the company addressed a known issue that was causing app or service failures and rendering Windows Server 2025 domain controllers unreachable after a restart.