Microsoft has released the following KB article:
Application contents are duplicated in stand-alone media in System Center 2012 R2 Configuration Manager
Symptoms:
Application contents are duplicated in the client cache folder for every Install Application step that is used in a task sequence in Microsoft System Center 2012 R2 Configuration Manager. This affects only clients that are deployed by using stand-alone media.
For example, a task sequence is created that has two Install Application steps, and each has a separate .msi file:
Install Application: Application2.msi
On the client that is installed by using this stand-alone media, the client cache folder (by default, this is Windows\CCMCache) contains two copies of each .msi file:
\Windows\CCMCache\1\Application1.msi \Windows\CCMCache\2\Application2.msi \Windows\CCMCache\3\Application1.msi \Windows\CCMCache\4\Application2.msi
Full details at:
Full details at:
http://support.microsoft.com/kb/2928122