P30 and HMRC online system

I have just had an email from a client saying that she has received a PAYE reminder notice - we have all had them.  Her email went onto say that she rang HMRC who told her no returns made since April 2011.

But on our computer system we have a copy of the HMRC page showing acceptance of nil returns forv the whole period up to September.  Salary started in Stember so payment of tax now made.

Am I alone with this problem or is there a failure in HMRC's systems?