When you enable WS-Atomic Transaction support on Server 2008 the installation gives you an info message in the installation log that states something to the effect:

<Informational>: To configure WS-Atomic Transactions, run the wsatconfig.exe utility in C:\Windows\Microsoft.Net\Framework\v3.0\Windows Communication Foundation using the following certificate thumbprint for the SSL certificate: 4EA4E7A5BE979E1039D2F6F51D77230843BED0D2

When you run the command it tells you to run you receive an error:

C:\Windows\Microsoft.NET\Framework\v3.0\Windows Communication Foundation>WsatConfig.exe -endpointCert:4EA4E7A5BE979E1039D2F6F51D77230843BED0D2

Microsoft (R) WS-AtomicTransaction Configuration Utility
[Microsoft (R) Windows (R) Communication Foundation, Version 3.0.4506.648]
Copyright (c) Microsoft Corporation.  All rights reserved.

Cannot update the WS-AT configuration when WS-AT network support is disabled.

The solution is simple. 

Reboot after enabling the WS-Atomic Transaction feature and then run the wsatconfig application again.

Use the full command line:

WsatConfig.exe –network:enable -endpointCert:4EA4E7A5BE979E1039D2F6F51D77230843BED0D2

Obviously replace the thumbprint with the one listed in your log.

Interestingly enough, Server 2008 spits out the message:

[Paraphrased]
The certificate could not be used..

So a subsequent execution of the same command rendered:

Could not find the specified SSL certificate.