Application doesn't work if it's installed using Application Template to a container with User Experience Virtualization (UE-V) installed. Meanwhile, application works fine if installed to a container without UE-V.
UE-V Agent is highly integrated with Windows. It requires .NET Framework 4.0 and PowerSell 3.0 to be pre-installed, which alter Windows environment significantly.
By default, any application template is created for a basic container with default environment. Thus such application template may be incompatible with a containers where UE-V agent is present, because container is too different compared to the basic container.
In order to use various application templates on containers where UE-V is installed it will be necessary to create special UE-V edition of these templates. Such application templates should be created on a container that has UE-V agent and its requiremenets (.NET 4.0 and PowerShell 3.0) already installed prior to "Application installation" step, on a "Preparation" stage.
NOTE: reboot is required to complete installation of UE-V Agent, it should be performed on a Preparation stage as well