When Microsoft released Exchange 2013 SP1, the hope was that quality had become the priority. However, we know now that several bugs were allowed to slip thorough QA unnoticed. This has been highlighted especially with the Transport issue that is referenced in KB2938053. So what is the issue. Direct from the Kb article:
After you install Microsoft Exchange Server 2013 Service Pack 1 (SP1) or you upgrade an existing Microsoft Exchange Server 2013 installation to Exchange Server 2013 SP1, third-party or custom-developed transport agents cannot be installed correctly. Additionally, the Microsoft Exchange Transport service (MSExchangeTransport.exe) cannot start automatically. Specifically, you cannot enable third-party products that rely on transport agents. For example, you cannot enable anti-malware software or custom-developed transport agents.
When the installation fails, you also receive an error message that resembles the following:
The TransportAgentFactory type must be the Microsoft .NET class type of the transport agent factory.
This problem occurs because the global assembly cache (GAC) policy configuration files contain invalid XML code.
Microsoft has developed a PowerShell script that corrects a formatting error in the configuration files that govern the Transport Extensibility that is built into Exchange Server 2013. To have us apply this script for you so that Transport Extensibility and third-party products that use this capability function correctly.
Many MVPs and MCMs have written about this to get the word out that after applying Service Pack 1, you may need to apply the fix described in KB2938053:
The real issue is that this problem, as Tony notes in his blog entry, is not well documented. With an issue like this where mail flow is affected, customers should be notified in a EHLO blog update or some kind of qualifying communication that would help their customers. Instead, Microsoft has not chosen to do so and essentially forces the customer to either search for a fix or flood Microsoft Support with calls.
*** UPDATE ***
Before I could even finish the article a bit of a discussion between Microsoft and the community resulted in a change in the visibility of this hotfix:
Thanks Microsoft for listening!