This issue is usually discovered through a process similar to the following:
This issue is almost certainly caused by a specific configuration within the Software Update Point(s) properties in Configuration Manager when the 'Enable third-party software updates' option is checked under Administration > Site Configuration > Sites > Right-click the site > Configure Site Components > Software Update Point > Third-Party Updates. If the 'Configuration Manager manages the certificate' option is checked as below, this means that Configuration Manager will check the signing certificate with every WSUS sync, and if it is not a WSUS self-signed certificate, it will replace it with a self-signed certificate.
There are two options to resolve this issue:
Either of these options will stop the Configuration Manager console from overwriting the existing certificate and allow you to keep signing updates with your custom certificate as intended.