In essence, the Flame malware appears to have code signed by a valid MS certificate authority. As this particular malware is suspected to have been written by a "state actor" (a.k.a. cyber-warfare unit for a government), chances are good that this CA is not circulating in the general unseemly underbelly of the Internet. However, it does present a compromise of those certificates, so Microsoft is issuing revocation certificates for them.
The core problem here is that this CA is trusted by all Windows installs by default, and could be used to sign patches or other software. This has obvious problems in the form of valid-seeming software installs, but less obvious ones in that somewhere a state-actor has the ability to perform man-in-the-middle attacks for SSL using valid certificates.
The PKI system was designed around the idea that certificate authorities would occasionally get compromised and does contain mechanisms for handling that. However, those mechanisms are not frequently exercised so the process of issuing such a revocation is, shall we say, not as smooth as it really should be.
You really should apply this patch as soon as it arrives.