My printer is a prusa i3 with auto levelling running marlin.
So this is what's happening: my printer heats up and then levels the bed normally, but after that - when the printing process actually begins - the Z height goes up to 0.35 no matter what Zoffset or slicer I choose I can't make it go down to the correct Z printing position.
In your slicer set Z offset to -0.35. So it will moves your nozzle down 0.35 mm to touch the bed.
If you can't do that , go to marlin configuration.h and comment out #define MIN_SOFTWARE_ENDSTOP_Z to become like this