I had this issue earlier and there is very limited comments about this on the web.
Using RemoteApp to publish an application to the desktop, when the App opens a subsequent window (ie. it opens a print preview window) it removes the focus from the main RemoteApp (as it should) however on closing the new window, focus is not returned to the previous window and doesnt trigger a screen redraw.
The impression to the user is that the app has frozen and requires you to click on the icon in the task bar in order to revive it. In actuality, it is simply refreshing from the screen redraw of gaining focus.
There is a fix on the Microsoft website - a HotFix: 967885.
I hope this helps someone.