Why is notepad++ blocking my autohotkey shortcuts?

For me, it was enough to restart Notepad++, so try that first.

Embarrassingly enough, I restarted my PC and now it's back to normal. I have to learn to do that before asking here...

I think autohotkey will fail to load the keyboard hook unless you run it as admin. If this is the case your keys won't work when another app (notepad++ or otherwise) has focus.

(I've experienced this behaviour (albeit intermittently) on autohotkey and winamp)