Of course they paid it to the Government; the Government has simply forgotten, or the news is yet to travel from the hand that received it to the dinosaur-like brain.

This happens all the time, just wait a while, it will resolve itself. I got letters saying I had to pay late fees even though I had submitted a nil return; after a while the system got into synch.

As long as you have payslips proving you had PAYE deducted, you won't have to pay it. If Revenue want to appoint agents to do their dirty work for them, they have to take the risk of the agents not doing their work properly. After all, you'd far rather be paid your full whack and then pay your tax when you're good and ready, but Revenue won't allow that, so let them suffer the consequences.

Make sure the NI number on the Reed payslips matches that on hte tax return.