Our developers have just found a solution to the problem with transport agent failures caused by Exchange Server 2013 SP1 update further described in this post. Microsoft is currently working on an official fix, but if you need a workaround right now, you can resort to instructions from our KB article.
The problem stems from improper formatting of assembly redirection policy files, which makes them unrecognized as valid XML files. Removing one invalid comment line from two config files located in the GAC folder fixes the problem.
Please note that we strongly recommend that you back up these config files before you make any changes.
Let us know in the comments or contact us directly if you have any questions.
EDIT: Microsoft has just officially confirmed that the issue is caused by SP1: support.microsoft.com/kb/2938053