I don't understand my Tax Free Amount calculation

I'm trying to understand my tax free amount calculation. I submitted some changes to HMRC to make sure that my PAYE deductions cover my interest and dividend income. They made the changes and send me a new Tax Code, and on their website I can look at the calculation. I don't uderstand it. They show my tax free amount, then the additions for pension payments and gift aid, and finally the deductions for extra income like State Pension, rent, interest and dividend. At the end it shows my new tax free amount. So far so good. The problem is that they start off with a tax-free amount of only £6,500 instead of £12,500, and so the final tax free amout and tax code is completely wrong. Now, my adjusted Net Income is just a few hundred punds over £100,000 so I get that the starting tax free amount is going to be a bit less than £12,500, but surely not half? I tried phoning about this, and after waiting for 40 minutes I got through to a lady, only for the connection to be cut after just a few words were spoken. We had barely said hello. I just can't face having to go through this interminable wait again, so I thought I'd ask here. Perhaps I'm missing something obvious?

Just to add something: this morning I phoned HMRC again to talk through this. After waiting for 40 minutes I got connected to a person. She asked some quetions about my interest income, then said she put me on hold to check something, and left me waiting for 15 minutes - and then I got a message saying 'thank you for your call' and the call was ended from their end. Just like that. So I've wasted another hour of my life. What an appalling level of service this is, and I still don't understand my tax code calculation.

Hi,
Without seeing the actual specifics of your tax record, it will hard for me to really provide an actual reason for this.
It could be your estimated income we hold is higher than you have stated, so it might need adjusting?
It could possibly be your tax free allowances have been split? maybe if you have a 2nd source of income? I can only apologise for the issues you have had contacting our helplines of late.
Have you checked via your PTA as you can review and amend certain aspects of your tax code using this. Personal tax account: sign in or set up.
Thank you.