Did you pay estimated tax evenly thru the year or a bigger payment for the 4th quarter due to the Roth conversion?
The IRS penalty calculations assume your income and payments occur evenly so if your AGI is increased due to the Roth conversion in the 4th quarter that is by default smoothed out over the year - so you are probably getting a penalty because it thinks you underpaid for Q1, Q2 etc even tho by the end you paid the total safe harbor amount.
If this is what's happening you can reduce the penalty by adopting the "Annualized Income" (AI) method under "Other Tax Situations" / Underpayment Penalty which feeds into Form 2210 that is used to convey uneven timing for large unplanned taxable events like Roth conversions or large capital gains.
You'll need to calculate and provide AGI etc thru the year as of 3/31, 5/31 and 8/31 for this method. Recommend checking the outcome on Form 2210 and there should be a worksheet which explains any residual penalty (this method may penalize you for any other misalignment in your AGI vs. payments where you were benefiting previously but should significantly reduce the penalty if not eliminate it).
Not a CPA/Expert just my 2 cents dealing with same issue.
