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 ?
Karabiner does not work with Sierra. The developer of Karabiner is working on a stripped-down version of Karabiner called “Karabiner Elements” which does work with Sierra. I’m using the beta version right now, which fixes some, but not all of my Sierra pains. When work on Karabiner Elements is finished, the developer wants to update the “proper” Karabiner to provide Sierra support.