Interest on late payments on account

Is it OK for HMRC to charge interest on late  Payments on Account?

Background:  Client very late submitting 2010-2011 tax return -- it was submitted in December 2012, a few days before submitting the 2011-2012 return.  Therefore, it could be argued that the estimate used for working out the payments on account is irrelevant.  Of course, one could argue this or that, but it is what the Tax Management Acts prescribe that is important.  Hence the question.

Other information:  Client has paid £1,300 in fines.