Okay, If you are able to replicate your testing with logging data, I should be able to help you out once I see the logging data.

Diagnostic → Logging and hit the play button. Once you do that, the logging will start recording. You can save or copy the contents and either send the file or the text over.

I uploaded two logs. In the first log, at the beginning I jogging the x,y, and z motors and then I turned on the HC, switched to manual and tried to move the Z axis using the UP and DOWN buttons on the screen.
In the second log, at the beginning I jogging the x,y, and z motors and then I turned on the HC, switched to PINS and tried to move the Z axis using the input signal.

Okay, I'm going to need two other things from you..
1. the .set file your version of Mach is using.  I see data about the screen commanding up and down is in the screen. This .set can be found in C:/Mach4Hobby/Screens It's probably one one the ones that does not start with "wx"
"
2026-04-13 13:13:50.147

• [I    ] - Screenset H.C. Manual Commanding Down 

2026-04-13 13:13:51.658

• [I    ] - Screenset H.C. Manual Commanding Hold (~D) 

2026-04-13 13:13:53.197

• [I    ] - Screenset H.C. Manual Commanding Up 

2026-04-13 13:13:54.923

• [I    ] - Screenset H.C. Manual Commanding Hold (~U) 

"
These aren't standard MachAPI's

2. m3 script. You can find this in your C:/Mach4Hobby/Profiles/{Profile Name}/Macros/m3.mcs
This will tell me what is being called anytime you run an m3 script. If it doesn't exist, just let me know.