By using scan codes instead of names hotkeys now overlap so for example 'numpad 1' and 'END' are considered equivalent so assigning either as a hotkey makes both work.
This was intended to avoid numpad keys from overlapping with regular numbers on top of the keyboard (this was an issue for me in one of the games I used when testing this).
I think fixing this will involve either rewriting more parts of the keyboard module or just entirely writing a hotkey system from scratch (more tempting as I keep running into things like this).