Following SP1 being installed I noticed that the task sequence that imaged our computers using USMT was not restoring the data. Also, it was not installing the applications that were defined as part of the task as well as skipping a few other bits and pieces.
The solution was very easy and if I had just followed my project plan it could have been avoided! I had forgotten to update my task sequences to install the new Configuration Manager client. Worth noting that I did not need to create this application as the SP1 installation had already done this.