PAYE Basic Tools overpaying Director tax and FPS confusion

I am a director of a company that was set up last year. I took no payment until the end of the year and then paid myself a lump sum, through the PAYE basic tools, that fell below the threshold for triggering tax or National Insurance. The P60 showed that tax was due as did the PAYE section on HMRC company screen. Given the deadlines, we paid this with the idea that we could sort it out in slower time. Various calls to HMRC have resulted in a number of alterations and cancellations to the initial final submission and now I'm completely confused. My P60 shows a nil payment for the year, any amendments to the FPS result in additional tax charges being raised, the company is shown as having paid tax (that wasn't due so needs to be credited) and my personal tax account shows that the amount I paid myself was taken as a monthly sum rather than an annual one. I've tried calling HMRC to sort it out, but no one seems to know how and as nothing is 'instant' I have to wait for days after changing something, then finding out it's wrong or hasn't worked, then call back to try to sort it all out. I think I have to change the FPS again, but even when I change the salary to an annual one, more tax is triggered and I fear that my personal tax account will double my salary for that month. Perhaps I could cancel the whole thing, return the salary and just manage it afresh this year. I'm not sure where to go from here. Other than round in circles.

Hi Helen Carrick,
Without being able to look into your account we would not be able to offer any solutions. It is possible that because of the way your account was set up the system has treated your annual payment as if it is due to your each month and calculated the tax accordingly. Please contact us on 0300 200 3200 to discuss this in more detail.
Thank you.