If you are experiencing the above mentioned problem after installing Service Pack 1 for Exchange Server 2013, then you should probably download and install this fix (KB2938053):
Describes an issue in which the Exchange Transport service cannot start in Exchange Server 2013. This issue occurs when third-party transport agents do not load correctly.
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.
Microsoft released recently the Windows Mobile 6.1 POP and IMAP Send Mail Patch.
This behavior is associated with a feature that is introduced in Windows Mobile 6.1. The feature allows for mobile operators to specify an alternate SMTP server name that is used if e-mail messages cannot be sent by using the user-specified SMTP server name. If the mobile operator does not specify an alternate SMTP server name and if the Windows Mobile 6.1-based device does not connect, the e-mail account is corrupted and cannot send e-mail messages.
Scalable Networking Pack (SNP) is a feature that was introduced with Windows Server 2003 and that also exists in Windows Server 2008 (but it’s turned off by default).
Although SNP was a good idea, as it could improve network performance, it may have some adverse effects on Exchange (for more details, read Windows 2003 Scalable Networking pack and its possible effects on Exchange).
After the report of these problems, Microsoft released a hotfix that would disable SNP features. A new hotfix has now been released, if you installed the first one, I strongly advise you to go and get this new one.