No, your first mistake was buying the program. As I've said many many times before, you only should be using speaker design programs if you know how to do it by hand. That way, when you get interesting/outrageous results, you already know what they mean and can decide where to go from there. It's like needing to be able to drive a manual transmission and buying a sequential gearbox car. Some of the features are now automated for you, but if you don't know what's going on behind the scenes, you won't understand what gear to be in, how to apply throttle properly to take off smoothly and how to downshift under braking. Same thing applies. I suggest getting some literature such as the Loudspeaker Design Cookbook and reading up before going into the program.
So with that said and to answer your questions, no, you're likely doing something wrong or improperly using a feature. A small ported box is simple to design, so I suggest doing it by hand first and then you can start using the program to fine tune how you want the speaker to behave in specific ways.