We've just checked and we're definitely measuring it correctly. The measurement is from BB to top of the saddle and both our measurements are out by quite a lot.
As an example, her current comfortable riding position is 74cm, yet the fit calculator is recommending around 64cm.
The inseam measurements you entered, did you take those as directed with a level or stiff book hard up against your crotch? You can't just use a trouser inseam.
Not a chance. Is it not something like you're measuring from pedal axle to seat and the site is giving you a BB to seat measurement?