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Source: Microsoft Support
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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.
This occurs because the TS RemoteApp points to SFTTRAY.EXE as the program to be run and the only files that can be used for icons when configuring a TS RemoteApp are DLLs and EXEs. Microsoft App-V utilizes the ICO file for the specific application when displaying an icon for virtualized applications.
This behavior is by design.
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