Yes, Lisa, this is fair ground for the nanny. But as you point out everyone has good points and bad points.
For example my current nanny (who I like very much), is very proactive (does things before I ask her to sometimes), is tidy and organised, is very committed to the job (always available for extra hours when requested), everytime I ask her to do something it is done without fail in record speed. Basically, she is fab and I love her.
But....
She is not very good on the nutrition front. She likes convenience food. She would expect her spag bol sauce to come in a jar and maybe add the meat to it at most. She LOVES garlic but can't be bothered to chop fresh garlic. Much prefers to open a jar and sprinkle (pour actually). She rips packages of cheese open so that they can't be neatly wrapped up to prevent cheese from drying out.
But still she is the best nanny I have ever had and I over look the other things because she does most things very well. DD's teacher and some of the mums and various mums from the gate have approched me out of the blue to tell me how good she is.
You do have have to take the person as a whole (especially when she is live-in!) and have realistic expectations. You can't expect perfection. But, on the other hand, you can expect her to do the job.
I think you should perhaps have a lighthearted chat with her and ask her what she would like to cook for the kids. Maybe she just wants to do it on her own time. Or maybe she wants to choose what to cooke rather than "Here. Chop this onion will ya." Or maybe she has never peeled an onion. If that is the case, then I'd leave her a variety of recipes as suggestions for things the kids like. You could even present it as "Since you just started you obviously don't know yet what the kids do/don't like to eat so I've prepared some recipes for you of things I know they'll eat." But don't go down to the level of telling her what to cook when.
BTW, I am most impressed that you whip up spag bol in the morning while kids are having breakkie. I pass mine over to nanny upstairs in pyjamas and leave breakfast, lunch, and dinner to her to sort out.