Sorry – I cleared the error by writing off the small balance owing on that invoice. Hence the problem has gone away.
One thing I have noticed in the past with the 2011 version is I had a problem with small rounding errors when filling in the invoice amount in the amount paid rather than just accepting the pre-populated field and processing the payment (on invoices paid in full). It was a if the prepopulated field had some hidden decimals that were taken care of with a full payment.
So on this with the problematic invoice I entered the part payment and a similar problem occurred.