I had a similar experience where I noticed, somewhat recently, that I was consistently .25mm above Z-zero. I would double check your mechanical setup, belt tension, v-wheels, motor pulley set screws, etc… and also look into belt stretch calibration. C3D Tutorial. I also found the tutorial for calibrating with calipers helpful too, if you have a set.
Calibrating for belt stretch changed the Z-zero, but I hadn’t dialed in everything as well as I could have since I noticed inconsistencies in steps when the Z-carriage was higher afterwards. I would have worked on it more, but was able to take advantage of HDZ availability and haven’t had issues with the BitZero since; this is why I suspect that in my instance it was something more mechanical.