Microsoft Application Virtualization KB article published last week, looks at an issue you might run into if you try to change the icon of a virtualized app when publishing it as a Terminal Server RemoteApp: “When a program that has been virtualized using Microsoft Application Virtualization (App-V) is configured as a Terminal Services RemoteApp in Windows Server 2008, the icon for the program is displayed as the standard App-V icon instead of the icon normally associated with the virtualized application.  You are also unable to change the icon to use the proper ICO file for the app.”

More info: KB970831