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10.1 ISE - Newly created source files do not appear in the Project Navigator Source window
This is a project refresh issue. Although the source gets correctly added to the project, the Graphical display does not get reset.
To fix the display, close and reopen the project.
This problem has been fixed in the latest 10.1 Service Pack available at:
The first service pack containing the fix is 10.1 Service Pack 1.