As discovered and documented by Daniel Larson, SharePoint MVP, the SharePoint Infrastructure Update changes the availability of SPContext. Previously one could leverage the IHttpHandlerFactory in order to obtain a reference to SPContext. Now it must be done in the IHttpHandler.ProcessRequest method. For more details please see Daniel's excellent explanation. This is actually not a bug, but a fix that was by design. If you are leveraging the SPContext in the IHttpHandlerFactory that logic should be transitioned over to IHttpHandler.ProcessRequest as this will be the supported method moving forward.
Sr. Application Development Consultant, MCSD.NET, MCTS