Ender 3 Pro Z-Axis Issue troubleshooting

New to the forum because I'm doing some troubleshooting for my son. I haven't been able to find this issue described elsewhere. Sorry for the long post, just trying to be thorough.

He's had an Ender 3 Pro for just over a year now - Marlin bugfix-2.0.x, 2021-12-07. BTT SKR Mini E3 V3.0 board - and we're running into issues with Z axis positioning. Something is preventing the Z home from being set at it's actual zero position.

The couple ways we've experienced this issue:
-Before we start any print, we have to manually position the Z axis at the bed by disabling the stepper motors. But upon starting the print, the Z-axis raises up off the bed, runs what I've assumed is an extruder purge along the Y-axis, moves over to the print location, but then does not drop back down to the bed. If the print is paused, the extruder is moved to a rest position (X = 0, Y = max, Z = same height) and there is not an option to disable the stepper motors so we can drop the nozzle back to the bed. The only option for adjusting the Z-axis is in the positive direction. With the factory motherboard, this same issue would occur, but the print could be paused, the nozzle would stay in the same position, and we could disable the steppers and drop the Z back down to the bed.

-When just trying to configure - not printing - I can disable the stepper motors and bring the Z down to its lowest position (right at the limit switch) and try to 'Set Home Offsets', I get a message that says 'Home XYZ First'. But when I Auto Home, the Z raises up approximately 6mm. If I go to adjust the Z axis using the screen and controls, I can only adjust in the positive direction, raising it up higher. The really weird part is that if I 'Auto Home' again, the X and Y both return to zero but the Z raises up another 6mm and I cannot lower it using the controls. I can only lower it by disabling the steppers, but then the described cycle starts over again.

The Z-limit switch seems to be positioned well, no Z-probe currently installed. I've dinked around with Z-offsets a bit, but those don't seem to actually address the issue.

My assumption is this is a code issue that needs to be resolved, but it's beyond my basic understanding of that. I recently installed what I thought was the most recent firmware for the board, but I'm probably missing something there as well.

Any insights are greatly appreciated, especially considering the machine can't currently print and my 11 year old is pretty frustrated about what is currently a fancy paperweight.