On the test client that I set up, I used very minimal entries.  No prior year information, single, date of birth 01/01/1960, California resident.  Wages of $3,000,000 with zero fed or state withholdings.  Lastly, no federal estimates, for California Q1 is $3,000, Q2 is $4,000, and Q4 is $3,000.  Just for completeness, I also didn't bother indicating that the taxpayer had the required health insurance.  

So, based on the information above, CA total tax liability is $372,937, estimated taxes of $10,000, ISR penalty of $3,468, and a CA underpayment penalty of $7,953 for a CA total balance due of $374,358.  Note that on page 5 of Form 5805, part II, lines 10 and 11 for column B are filled in.  Line 10, column B shows 169 days and line 11 shows $3,099.65.  This looks correct.  I can manually replicate all of the calculated numbers.

Now, here is the issue, if I simply add $10 of CA income tax withholdings, the CA underpayment penalty drops to $4,853!  If you look at page 5 of 5805, part II, lines 10 and 11 for column B are now blank.  There is no way this can be correct?

What worries me, is it is not as simple as Lacerte just didn't calculate the penalty at all, which would be easy to catch.  This is simply, understating the penalty due to a program error, which could have easily been missed.