The short answer, explained
HMRC charges interest on tax paid late, calculated from the date the tax was originally due, not from when an enquiry uncovered the underpayment.
The rate isn't a fixed percentage set once and forgotten. It's linked to the Bank of England base rate and moves whenever that rate changes, so the interest you're charged today may differ from the rate that applied when the tax first fell due.
This interest is separate from any penalty. Even where no penalty applies, because you took reasonable care, interest is still due on tax paid after its due date.

