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Microsoft Intune Certificate Connector Failure

The Microsoft Intune Certificate Connector enables the provisioning and de-provisioning of on-premises PKI certificates for Intune-managed devices. Always On VPN administrators using Intune to deploy certificates with the Intune Certificate Connector using either PKCS or SCEP may encounter a scenario where certificates are no longer being provisioned to users or devices after working reliably previously.

Certificate Not Found

When this issue occurs, users will no longer be able to access the VPN and receive a “certificate could not be found that can be used with this Extensible Authentication Protocol” error message.

Connector Status

To determine the status of the Intune Certificate Connector, open the Microsoft Intune Admin Center (https://intune.microsoft.com) and navigate to Tenant Administration > Connectors and Tokens > Certificate Connectors. The status of the certificate connector server will be in Error.

Event Log

Open the event log on the server where the Intune Certificate Connector is installed. Navigate to Applications and Services Logs > Microsoft > Intune > CertificateConnectors > Operational. Here, you will find a variety of warning and error messages.

Event ID 5001

This is a warning from the CertificateConnectors source with event ID 5001 in the Task Category HealthMessageUploadFailedAttempt with the following details.

PKI Create Service:

Failed to upload health messages. Requeuing messages.

Event ID 1003

This is an error from the CertificateConnectors source with event ID 1003 in the Task Category PkcsDownloadFailure with the following details.

PKI Create Service:

Failed to download PKCS requests.

Event ID 2

This is an error from the CertificateConnectors source with event ID 2 in the Task Category Exception with the following details.

PKI Create Service:

Microsoft.Intune.Connectors.PkiCreateProcessor.Process threw an exception.

Expired Certificate

The warning and error messages recorded in the event log indicate an expired certificate on the Intune Certificate Connector server. Open the local computer certificate store (certlm.msc) on the server where the Intune Certificate Connector is installed. Review the expiration date of the certificate issued by Microsoft Intune ImportPFX Connector CA. It is most likely expired.

Click on the Certification Path tab to view the certificate status.

Renew Certificate

To renew this certificate, you must reinstall the Intune Certificate Connector. However, you do not have to uninstall it first. To renew the certificate, navigate to C:\Program Files\Microsoft Intune\PFXCertificateConnector\ConnectorUI and double-click on PFXCertificateConnectorUI.exe. Follow the prompts without making changes to the existing configuration. You’ll be prompted for the service account password (if using a domain account) and proxy credentials (if using a proxy server). In addition, you’ll be asked to sign in to Entra ID (formerly Azure AD). Be sure to provide credentials that are a global administrator and have an Intune license assigned. Once the process is complete, a new certificate will be installed in the local computer certificate store.

Intune Configuration

After updating the Intune Certificate Connector, a new certificate connector appears in the Intune Admin Center. You can now safely delete the old connector and rename the new one accordingly.

Redundancy

Deploying multiple instances of the Intune Certificate Connector is an excellent way to avoid future outages! It’s also a good idea to stagger their installation by a few months to ensure that a future certificate expiration doesn’t result in lost functionality. If you’ve deployed Intune Certificate Connectors recently, consider updating them at rotating intervals so certificates expire at different times.

Additional Information

Intune Certificate Connector Configuration Failed

Intune Certificate Connector Service Account and PKCS

Intune Certificate Connector Configuration Failure

Microsoft Intune Learning Resources for Always On VPN Administrators

Always On VPN Disconnects in Windows 11

Always On VPN administrators migrating their endpoints to Windows 11 may encounter a scenario where Always On VPN randomly disconnects when the VPN profile is deployed using Microsoft Intune. The same configuration deployed to Windows 10 devices works reliably, however. In addition, Always On VPN profiles deployed using PowerShell (natively or with SCCM) or PowerON DPC do not experience this problem.

Troubleshooting

Administrators troubleshooting this issue will find the root cause is associated with the Always On VPN profiles being removed and replaced each time the device syncs with Intune. This occurs even if there are no changes to the configuration. Removing and replacing the Always On VPN profiles on each device sync is unnecessary, of course, but is also highly disruptive to connected users.

Intune and XML

The Intune team identified the issue, and a fix was made available in the August update. However, many of you have reported the issue persists with some Windows 11 clients after installing the latest updates. Further investigation indicates that although the issue has been resolved when using Intune and the native VPN device configuration profile template, the problem still occurs when using the Custom device configuration template.

Workaround

Microsoft is aware of the issues with deploying Always On VPN client configuration settings using XML in Intune, but there’s no indication when or if they will fix it. Until then, administrators have two options to address this problem.

Native VPN Template

When deploying Always On VPN client configuration settings to Windows 11 endpoints, use the native VPN device configuration template, as shown here.

Using the native VPN template does have some limitations, however. The following settings are not exposed using the native VPN template and can only be configured using XML.

Disable class-based default route
Application-specific traffic filters
IPv6 routes (UI doesn’t allow /64 prefix!)
Exclusion routes
VPN protocol preferences

XML

If you must use XML, I’ve had some success by ensuring the order of XML settings is exactly as Intune expects. Follow the steps below to confirm the XML settings order in your XML configuration file.

Deploy your XML file with Intune.
Run Get-VpnClientProfileXML.ps1 to extract the deployed XML settings.
Compare the order of settings to your existing XML.
Make changes to ensure all settings in your XML are in the same order as the extracted XML.
Publish a new XML configuration file using Intune and test.

I’ll caution you that this workaround doesn’t always work reliably. Some customers report that this solved their problems entirely, while others have indicated it does not. My testing shows the same results. Let us know in the comments below if this works for you!

Additional Information

Always On VPN Windows 11 Issues with Intune

Always On VPN PowerShell Script Issues in Windows 11

Always On VPN and Interface Metrics

In Windows, each network interface identified by the operating system is assigned a metric value. Interface metrics are settings that determine the priority or preference of network interfaces when there are multiple active network connections. The Windows networking stack uses these metrics to determine which network interface should be used for routing traffic when multiple network interfaces are available. Network interface metrics are critical for Always On VPN administrators to understand because they can impact how name resolution requests are processed when an Always On VPN connection is established.

Metric Values

By default, Windows automatically assigns metric values to network interfaces (including VPN interfaces) based on various factors, including the connection speed, link state, and interface type. It tries to select the most suitable interface for general internet connectivity.

Metrics and DNS

Windows will also use the network interface with the lowest metric value as the preferred interface for sending DNS queries by default. This means that DNS queries will be routed through the network interface with the lowest metric value, assuming it is available and connected. When an Always On VPN connection is established, DNS queries may fail or return unexpected results if the network interface metrics are not configured optimally.

Split DNS and Wired Ethernet

Split DNS (sometimes called ‘split brain DNS’) is when the DNS namespace is the same internally and externally. The most common scenario where interface metric settings interfere with DNS operation is when using split DNS and the endpoint is connected to the Internet with a wired Ethernet connection. In this scenario, the Ethernet interface will be assigned the same or lower interface metric value as the Always On VPN interface, which can yield unexpected results.

Viewing Metrics

Always On VPN administrators can view currently assigned interface metric values by running the following PowerShell command.

Get-NetIpInterface

Assigning Metrics

Most Always On VPN administrators will never have to change interface metric settings. However, if your implementation uses split DNS and some of your endpoints connect using wired Ethernet connections, you may need to update the interface metric settings to ensure proper DNS operation. Choose a setting for the interface metric value that is lower than the wired Ethernet interface. I’ve used a value of ‘3’ without issue for many years. Use one of the following methods to update the interface metric for Always On VPN connections.

PowerShell

Updating interface metric settings in Windows can be accomplished by running the Set-NetIpInterface PowerShell command.

Set-NetIpInterface -InterfaceAlias <connection name> -InterfaceMetric 3

Note: Using PowerShell to assign the interface metric is not persistent! While this method is suitable for local validation testing, you should use one of the following methods to implement this change permanently.

Rasphone.pbk

To assign the interface metric permanently, Always On VPN administrators can edit the following settings in the rasphone.pbk configuration file.

IpInterfaceMetric=3

Ipv6InterfaceMetric=3

Administrators can automate updating this setting using the Update-Rasphone.ps1 PowerShell script. In addition, the following scripts can be used with Microsoft Intune remediation.

Detect-DeviceIpv4InterfaceMetric.ps1

Remediate-DeviceIpv4InterfaceMetric.ps1

Detect-DeviceIpv6InterfaceMetric.ps1

Remediate-DeviceIpv6InterfaceMetric.ps1

Detect-Ipv4InterfaceMetric.ps1

Remediate-Ipv4InterfaceMetric.ps1

Detect-Ipv6InterfaceMetric.ps1

Remediate-Ipv6InterfaceMetric.ps1