Due to a problem in Quartus® II Software, when you open netlist viewers from the Tasks pane, Analysis and Elaboration is run before opening the design in the RTL viewer. This happens when you compile the design from the command line. The task pane has no knowledge of the compilation status and forces Analysis and Elaboration to be run again.
To work around this problem, launch the RTL viewer directly from the Tools->Netlist Viewers->RTL Viewer menu.
This problem is scheduled to be fixed in a future release of the Quartus II software.