Incorrect Tax Assessments - why is nothing being done?

I have today received (from my client) a copy of tax calculations for 2008/09 and 2009/10 showing refunds due, because the PAYE computer has spewed out a calculation showing the pensions but not the self-employment income.  This is the thrid client this has happened to this month.

If I submitted a tax return excluding the self-employment income my client would have an enquiry, would have several tortuous months and would then have to pay penalties and interest at the end of it all.  If they make a mistake, we have to run around getting them to sort it out and then feel grateful.

There is clearly something wrong with their computer at the moment.  Why is nothing being done?