Microsoft published Microsoft certification authority signing certificates added to the Untrusted Certificate Store on the Technet Security Research and Defense blog providing some more details on security advisory 2718704. Quoted from the article:
How did this happen?
When we initially identified that an older cryptography algorithm could be exploited and then be used to sign code as if it originated from Microsoft, we immediately began investigating Microsoft’s signing infrastructure to understand how this might be possible. What we found is that certificates issued by our Terminal Services licensing certification authority, which are intended to only be used for license server verification, could also be used to sign code as Microsoft. Specifically, when an enterprise customer requests a Terminal Services activation license, the certificate issued by Microsoft in response to the request allows code signing without accessing Microsoft’s internal PKI infrastructure.
On the relationship between this vulnerabilty and "Flame":
Connection to Flame malware
Components of the Flame malware were signed with a certificate that chained up to the Microsoft Enforced Licensing Intermediate PCA certificate authority, and ultimately, to the Microsoft Root Authority. This code-signing certificate came by way of the Terminal Server Licensing Service that we operate to issue certificates to customers for ancillary PKI-based functions in their enterprise. Such a certificate could (without this update being applied) also allow attackers to sign code that validates as having been produced by Microsoft.