All my applications and packages worked in my TS deployment apart from 2, both were packages.
I added a reboot in to the task sequence and this seemed to fix it. Simple, but there you go.
This fixed it for me, but I just had to understand why packages were successful, but Applications were not.
It is because Applications have dependencies and Detection methods. Essentially, the reboot fixes it because it then boots into proper Windows (be sure to select "the currently installed default operating system" radio button in the restart computer task) and this environment is capable of detecting the dependencies and detecting a successful install.
In my case, I have a few driver packages that reboot into Windows before installing applications, so I added the mirror opposite WMI query into my reboot task to ensure the computer isn't rebooted twice (another way would be to use a query that would detect if the machine was already in Windows Proper, but perhaps someone else will post that query).