XT-3 Focusing Issue

Hello,

I just sold my old Canon 6D + gear to purchase the Fuji XT-3. I had the X100S and then the X100F and enjoyed the image quality so much that I decided to upgrade. I've never been impressed by the X100's ability to focus (although the X100F made some advancements on that front) but all the reviews touted the XT-3's amazing AF system so I was excited to start shooting with it. I took it out of the box, upgraded the firmware through the app and then took some shots of my daughter walking around. It wasn't particularly bright, but diffused daylight was coming through a big window and hitting her right in the face. AF-S and everything was on Auto except aperture  which was set to 1.4 on my Fuji 56mm 1.2. I halfway pressed the shutter, heard the beep, and fired a few shots. 9/10 were blurry. Buyer's remorse immediately set in. Since then, I have customized the settings and been able to get more sharp images with AF-C and Face/Eye detection on, but if I'm using AF-S, depressing the shutter to get an AF lock seems to produce out of focus images. In fact, I enabled pre AF (which allows the lens to focus on whatever your square is hovering over without pressing anything) and after the pre AF produces a sharp subject, depressing the shutter half-way and locking the focus would render the subject out of focus again. Did I get a lemon or does the XT-3 require some effort to focus properly? Is there a test I can perform? Please advise. Thanks!