I found an odd issue in SCCM 2012 SP1. I have many applications that install perfectly when deployed. There is no source for the application because it is a network based install, and needs to be. If I try to add the application to the"Install Application" method in a task sequence, it looks successful. But then re-edit the task sequence and it will tell you there is an issue with the "Install Application" method. The app will not install when you run the task sequence either. If you then add a content folder to the application, it works like a charm.
In the meantime, I am providing a dummy content location for these apps so I can get things running. But has anyone run into this? Seems so odd that task sequences don't like apps without content.