MSBuild Custom Publishing not Transforming Web.config files

I am using this solution to perform my Publishing via MSBuild and Jetbrains TeamCity: http://sedodream.com/2013/09/21/HowToExtendTheWebPublishProcessWithoutModifyingProjectContents.aspx

For the most part, this works just fine in terms of getting the content published, however, I am encountering one problem with the solution in that it is not performing my Web.config transformations!

Every other aspect of Publishing is working according to expectations excluding the Web.config transformations.

I am using MSBuild that ships with Visual Studio 2013.

Please advise as to what I may be doing wrong.

Thanks.