Not sure if I am diagnosing this correctly, but my impression is that KM may be having difficulty re-mapping simple keystrokes (other than function keys and combinations including ⌘⌥^ etc) under 10.12 Beta (16A304a)
There may be another explanation which I haven't spotted, but things like this are now passing the hot key straight through, rather than remapping it:
I notice that Karabiner is not yet able to work with Sierra betas, and I wondered if they were causing KM similar difficulty ?