Late submission of tax returns

Hi My client owned a number of properties, the first being purchased in 2001.  He came to me in 2010 and in May 2010 we finally submitted all the tax returns for the years 2001 through to 2009. 

The Tax office wrote to us in respect of 2001 and 2002 saying that we are outside the limit but they would treat it as if the return had been submitted on time.  They also wrote regarding 2007 and 2008. For these years there was some late filing penalties to pay which has been done but no other questions.

However, the tax for the other years 2003 to 2006 and 2009 has not been allocated and there is some £36,000 sitting as an overpayment.  We wrote in 2011 asking that they allocate various amounts to the correct tax years but nothing was done.  The statement on line shows that there is no tax liability and no tax due for these years.

Should we write and request that they confirm that the tax years are closed and that there is no liability due before requesting any repayment.  Would they respond to such as request? Is there any other strategy that we could pursue?

My client has since been submitting the tax returns on time and paying the tax as it is due.