Hi Huw,
Hi it is hard to say wothout seeing an actual breakdown of what your code or both sources includes, it could be that your 2nd pension straddles the BR/HR bands so your main code may have been adjusted to account for this.
But really we would need to check your personal records, which cannot be done via this forum, you should contact the HMRC helpline:
Income Tax: general enquiries,
Thank you.