I would move to the FTL assist method, which is built into IS Boxer, instead of the Focus assist method.
FTL works as well as Focus, and Focus is free for other options.

It sounds to me, you have one hunter set as focus, with the second hunter targeting their focus (the first hunter), and then being unable to shoot.

You could solve that with:
/assist [target=focus]
/cast Whatever Shot

If it was working in Burning Crusade, having gone to Northrend should not have changed anything.
Not sure why a change of location would break a macro.