Two suggestions.
First, as others have stated, confirm your inputs with actual measurements. Folks I've helped in the past have put in the wrong amount of center shot, thickness of the strike plate, and actual draw length. The results they get don't look like anything they see when they shoot. If the bow you are using is listed in the menu, then the centershot measurement is made for you. You will still need accurate input for the strike plate thickness.
If your input data is correct, then the second area is use of the 'personal form factor'. I encourage folks who have a current arrow setup that flies well, to put in all the measurements associated with that setup. Run the calculator. If the spine measurements are off by more than a couple of pounds, go to the personal form factor at the bottom of the input page. It will accept positive and negative values. So pick one and see if the spine measurements get closer together or further apart. Keep inputting slightly different values until the spine measurements get within a couple of pounds. Whatever 'personal form factor' you used that gets you close is the PFF you should use for all other bow/arrow combinations. The PFF is simply a way to customize the model to your way of shooting. If a PFF of '0' is used you are relying on the 'average' values used in the model. If you are not 'average', you will likely have to use a PFF determined by trial and error.
For example, if you have a 'perfect' release with your current setup that you know flies well, and use a PFF of zero, the results will likely show an arrow that is under spined. If you pluck the string like a you're playing a guitar, the PFF of zero will likely show over spined using the input from your current setup.
The PFF is a way you can customize the model to reflect how you shoot. Don't expect it to match anyone else but you. It's a great tool if used properly.