Well those all look appropriate. Is there an EMS in play by chance? I’d still like to see the M-1-2-1-3 set it to 5-1 and have someone push the hall button and see if you’re seeing the input.
Could wire in an RS board with buttons in the MR also.
I cannot think of anything else as to why the bottom hall button would function but not the rest. Especially if swapping the IO board fixed it.