Hi David,
When using the GUI, under the hood VSPAERO is launched pretty much the same as how you would do it yourself through command prompt. You can scroll all the way up through the VSPAERO output window, and will actually see the command that is send out to run VSPAERO - see attached image. As you can also see in this image, this command sends the Mach, alpha and beta lists at which the analysis should be performed and some settings you use for your aerodynamic analysis: start iteration for wake averaging, iteration to start calculating the wake and using the Jacobi preconditioner. Now, as you only use a single analysis point, the Mach, alpha and beta are also stored in the .vspaero file used when launching the analysis. Hence, when not passing these the solver will still solve at this flight condition. However, the AVG and SKIP wake iteration parameters are not stored in this .vspaero file and will have to be passed on through the command when you want VSPAERO to use them. Now I just noted that, even though the Jacobi preconditioner is stored in the .vspaero file, you still have to specify it manually, or otherwise it wont work. -- maybe Rob can tell if this is a bug?
When I run your case through command prompt whilst including the wake parameters and Jacobi preconditioner, I do get the same results as the GUI. However, when you do not specify these parameters, it will assume the default values for the AVG and SKIP wake iterations and the Jacobi preconditioner (=off); in this case you do indeed end up with the CL@-5AoA = 0.025. Actually it is only the Jakobi preconditioner that causes the difference I think. But at least this explains the differences you are getting between the GUI and Command prompt: they were actually running with different wake and preconditioner settings!
Regarding the density, and also flight speed velocity (they can be set in the .vspaero file, as well as in the GUI under the ROTOR tab): AFAIK they are not used in a normal VSPAERO analysis. They only matter when using actuator disks in your analysis, because they are used to determine the propeller performance, like thrust and power, based on the specified RPM, CT and CP.
Hope that clarifies,
Jasper