I have a director who is paying 2x£5000. On the first payslip there is not tax and NI. I don't understand why there is £165 tax due on the second one as his wage is under £10000 limit.
If you were to pay the director a £1 next month they should get it back. See if you can use the Tax Free Tables. If you're doing say February payroll then the director will be able to earn 10000 / 12 mths * 11 = £9167 tax free x 20% is £166.
The allowances are given month by month unlike the National insurance scheme for directors.