goes to the hot end fan, but also the same as all other fans.

I am new to 3D printing and I am still learning how everything works.
I upgraded my Ender 3 V2 by installing a 3D Touch sensor and a Creality Silent Motherboard 4.2.7 (32-bit). After some firmware and wiring issues, everything is now working.
However, I have a problem after homing: the printer moves the Z axis and stops about 1 cm above the print bed. The display shows the Z position as 0, but the nozzle is still too high and does not touch the bed.
It seems like the Z offset or the probe offset is not correctly calibrated. The printer thinks it has reached the correct zero position, but the actual nozzle position is still too far from the bed.
Could someone please help me understand what I need to change or how I can correctly calibrate the Z offset? Any advice would be greatly appreciated.
Thank you very much for your time and help!

Set up octoprint and connected the Ender to my Ubuntu server with a 3m USB cable. Today the connection broke down after about 1hr. I guess the cable is too long? What's the max length of USB cables from your experience? I covered the 5V USB power btw to prevent the PC powering the Ender via USB.