Tá siad ag rith fós == they are still running.
My intuitive response to Níl siad ag rith fós was "they are not still running", or "they are not running any more".
I realized that "They are not running yet" was the more likely translation, even though it means exactly the opposite.
Is that ambiguity there in Irish?
I asked two other people about this today - not native speakers, just "school Irish". They both had the same reaction that I had - "They are not (still running)" or "They are not running anymore", but conceding that "They are not running yet" is probably the correct translation.
But it can be used for "still" in this case - "they are still not running" means "they are not running yet"
The problem arises because the meaning of the English sentence changes depending on where you put the "not" - "they are still not running" means the opposite of "they are not still running".
You're reading the guidance :-)
Seriously, though, this is just one of those quirky little things that crops up when you are moving between languages. So you get it wrong the first or second time you encounter fós at the end of a negative sentence, maybe the 3rd time you remember that "hold on, there's something weird about fós in this situation".