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This is not a SilkTest problem. This is the way Terminal servers work. The terminal server will block the communication channel until the session is reconnected. This includes the graphic updates that Silk Test is doing on the status window and the running state on the main dialog. The update is effectively blocked thus preventing the application from continuing. While closing the status window will help the main window blinking the run indicator will cause it to block.
This means that if a script is running and the session is disconnected then the script will pause until it is reconnected again.