I'll have a look into it. Hacking at another part of the site right now so when I'm banging my head at the wall over that and I need a break I'll look into it and see whats up.
EDIT 1: Comfirmed in that sense that on my local "barebones" install shortcuts work. But they don't work on my test copy of the site (nor the live site). I'll see why and fix it.
EDIT 2: I believe its to do with having the categories on the "home" page. Using other discourse sites (LevelOneTechs/TwitchDev) when the category view is up the shortcuts doesn't work. So this looks like a "discourse" bug/feature. I'm sure I can code my way around it but the question now becomes is it a reported bug on the discourse software? if so are they going to fix it? (If I'm going to make changes I don't want to make changes that could break stuff down the road) etc.
EDIT 3: https://meta.discourse.org/t/keyboard-shortcut-k-j-doesnt-work-on-categories-page/15948 Basically its a reported "bug" but they still haven't fixed it because they not found an intuitive way to do it.
Sam's (co-founder of the software) idea is :-
j/k ... moves between categories
press tab on category, j/k moves between subcategories
press tab again, j/k moves between topics.
Suggestions on how it should work are welcomed. If we can decide on a way it should work then I'll code it in