TurboTax not applying estimated state tax payments to state return.

I am using TurboTax for Home & Business 2019. I entered my estimated tax payments for both Federal and California state correctly into TurboTax and the payments show up when I go into edit mode for that section in the Federal Credits & Deductions section. The Federal Estimates are applied correctly. However, when I applied a large 1099-R for which I had made these estimated payments, to my horror my State tax owing went from green to red with TurboTax telling my I had an underpayment penalty. I finally went to the forms and found that TurboTax had not populated my estimated state tax payments. When I manually populated the payments in the state form the tax owing went back to green which is what it should be. This is not the first time TurboTax has done this. Perhaps it would make more sense to prompt for state estimated payments at the start of the state processing as there seems to been a problem getting them credited from the federal processing side.