Pension Relief on both Tax Code and Self Assessment. Help.

I've just filled in my self assessment and it asks for gross personal pension contributions which I've put in. When it gets to the calculations it says my basic rate limit has been increased by £X for to £Y for pension payments meaning it is apply higher rate pension relief there. My problem is that I already get the relief in my tax code through the entry "Personal Pension Relief" which raises my personal tax allowance meaning I get the 20% additional tax relief there. I've spoken to people in both self assessment and PAYE about this and it appears that nobody has ever heard of this happening or is not aware of how to fix it. I actually want to pay the right amount of tax but self assessment is not letting me asking me for less instead.

Hi Darryl,
Inserting a figure for gross personal pension contributions in your return confirms the amount of Personal Pension Relief that should have been applied through your code for that tax year .I
If the amount you enter for gross personal pension contributions matches the amount of Personal Pension Relief in your code, no further relief than what you will have received in-year will be applied.
It will still show on your return calcualtion for illustrative purposes.
Thank you.