That kind of integration to the OS is normally not something ThinApp will provide automatically for you. I have no knowledge of this application but depending on how it makes this integration it will still be possible to have it even with the ThinApped version. Sometimes all that is needed is to place an Entry Point in the Start menu – Startup folder. Sometimes you will have to add keyboard shortcuts to the shortcut we create when you register the package. And sometimes is it just not possible to make it work. Application Virtualization is about protecting the OS from being polluted with physical installation so we can simply not add everything to the OS.

One thing that almost every time works is to launch a locally present application inside the virtual environment of your package but this means you must always run it in this way to have the functionality, making this not always a valid solution.

Read more at: http://communities.vmware.com/message/1509880