I was in a similar situation a couple of years ago. I was alerted to it when we had a change of management in the payroll department.
I phoned HMRC with my payslip details and previous P60's etc. and apart from it taking me about 45 mins to get through to someone it was a very painless process. The lady on the phone took my details and then checked back over the last 7 years for me. She found that I had overpaid tax for 3.5 years previous and organised a calculation to be done. I was told that I would receive a letter informing me of the calculation and the ammounts due back followed by a cheque within around 4 weeks.
4 weeks later a cheque for £3.5k hit the mat
/Salsa