Currently taking HMRC to the Adjudicator for exactly this problem. Over 4 tax years and 2 interim jobs, they have failed to put pension and salary information together and recoup tax on the element of income that fell into the higher tax bracket. This has led to over £7k in underpaid tax, despite full disclosure at the start of each job. Made a claim under ESC A19 which has been flatly rejected several times. The Adjudicator is snowed under atm and estimates it will be several months to come to a decision.
In the meantime the frequent switcheroony of my personal allowance from pension to salary and back again will no doubt continue.