So I have finally received a response from Intuit/Lacerte:

                "So it has been determined that Lacerte is working as designed. You would have to going to screen 18 and manually remove the tax refund amount if you do not agree with the amount. A product enhancement as submitted for a diagnostic I do not have a time frame on when that would implemented. I apologize as I know this has been a frustrating thing to deal with."

So, while waiting for an eventual reply, we have started overriding the automatic overpayment being taxed at 100% in a subsequent year after proforma'ing the tax return previous year, to be only $10,000 if applicable.  We will now take a look in the "off" season to see what the tax effect is on those clients who have filed in prior year(s), that we also missed, and have over-reported a prior year state refund.