For the last three years, my QCD has generated a cost of over $2000 increase in taxes against listing as RMD and using schedule A. What could be the reason?
Do you have basis in nondeductible traditional IRA contributions and the taxable amount of your traditional IRA distributions calculated on Form 8606 is less than the full amount of the distribution?
If so, the charitable deduction is probably reducing taxable income by more than the IRA distribution is increasing taxable income. This effectively lowers your taxable income over many years instead of lowering your taxable income by larger amounts in later years. A non-QCD distribution reduces the basis that would otherwise be available to apply to distributions in later years while a QCD comes only from otherwise taxable money in your traditional IRAs. Using the QCD approach would save you less in tax now over using the Schedule A deduction, but you would get a bigger tax savings in the future when only basis remains to be distributed (which cannot be reported as a QCD). By paying less tax now you get the time-value of the tax money saved at the front end, so using the Schedule A deduction may be better long-term. But you also need to consider what side effects you might have by having the higher AGI with the Schedule A deduction.