Non-executive directorships and PAYE

My wife and I are both chartered accountants and for eight years have operated through a limited company which we own 50:50 and of which we are both directors. Although I have a pratising certificate I do not actually practise as an FCA. We provide a range of services to SMEs covering out-sourced finance department activities through mentoring, leadership development and ad hoc consultancy eg succession planning. For four of the company's clients I have been appointed as a non-executive director and have always invoiced our total fees to our clients on a monthly basis. I believed that the concession ESC A37 covered such portfolio arrangements and that HMRC accepted the rationale of bringing all such income into our company where of course it is taxed, or it is paid to us and taxed upon us. However the auditors to one of our clients have got very agitated and are insisting that I should have two contracts with each of my clients - one would be a director's service agreement and payment under that would be through their PAYE schemes, whilst the other would cover the other services and would be invoiced from our company. Is our pragmatic approach to this issue going to create a problem? Should we be as agitated as our client's accountant?