Microsoft has just updated the following KB Article:
Content does not install or upload to the cloud distribution point when you create an application in CU1 for System Center 2012 R2 Configuration Manager SP1 or System Center 2012 Configuration Manager SP2
Symptoms:
Consider the following scenarios. In these scenarios, you run one of the following to create and deploy an application:
- Cumulative Update 1 for Microsoft System Center 2012 R2 Configuration Manager Service Pack 1
- Cumulative Update 1 for Microsoft System Center 2012 Configuration Manager Service Pack 2
Scenario 1
- You create an application to deploy to a mobile that supports .xap device type files.
- You locate the application properties in the Deployment Types list, click Copy to create an identical deployment type, and then click OK.
- You deploy the application and specify the content that should be uploaded to the cloud distribution point.
Scenario 2
- You create an application to deploy to a mobile device.
- You locate the application properties in the Deployment Types list, click Add to create a deployment type that has a framework dependency, and then click OK.
- You click Add again to create an additional deployment type that has the same framework dependency and then click OK.
- You deploy the application and specify the content that should be uploaded to the cloud distribution point.
In these scenarios, the content does not upload, and the application does not install.
Full details:
https://support.microsoft.com/en-gb/kb/3093596