You mention a P11D - what are you completing on that?
If you are paying £1000 Employers NICs, then nannies salary is a little over £15,000 gross a year?
But you say you are paying £1482 Net per month, so with a 1000L taxcode, 5 days per week, 40 hours per week, then I make that £21,806 gross a year, with Employers NI being nearly £2000.
MrAnchovy's PAYE Calculator
I can't get £494. I can get £495 so that is probably the thing (PAYE calculators are not precise, they are a guide) so to get that figure I used:
Monthly Net Pay £1482, Days per Week 5, Hours per week 40, Taxcode 1000L, No Student Loan.
The £495 is the total of: Employee Income Tax, Employee National Insurance, Employers National Insurance.
So that then begs the question, what is the other £1000 a year charge for, as it is NOT Employers NICs.
My gut feeling is that something is going wrong - maybe they are somehow seeing your nanny as being a benefit to you as a director (assuming you are a director). Maybe it is some kind of employer supported childcare directly contracted.
I would separate out your business from your household staff. Get different payroll agencies to do it. PAYEforNannies charges around £125 a year, sure it is more than you are currently paying but it is less if you get this strange £1000 charge for doing it via your company payroll provider.
I am not an accountant but it looks odd to me. So if your accountant can not tell you exactly how things are calculated, then I would worry as an accountant should be able to tell you.