I just dug through their discord and it looks like it's a known issue. Apparently the new update changed how the OEM keys function.

I wonder if it had to do with them adding the repeat function to those back keys

So it appears that either the new AC update or the microcode update broke functionality in handheld companion. 

I had my M1 button configured to bring up the quick tools menu. Post-update, I can no longer use that hotkey. HC doesn't even recognize when I press the M1 or M2 buttons. I tried binding the menu to multiple other sets of keys and the menu started popping up, even when those keys weren't being pressed. 

Has anyone else run into this?

New AC update or MCU broke handheld companion