If the program allows you to decline the penalty, I would do that, and wait and see if the IRS bills you.
The tax system is supposed to be pay-as-you-go, and if your payments don't keep up with your income, you can be assessed a penalty, even if you pay in full in time. My guess is the late conversion is being annualized, with the result that the April payment appears too low. But you would need to look at the actual form to see how the calculation is being made. Rather than fuss with it, I would decline the penalty and wait and see if the IRS bills you. You can then request a waiver for cause, or if this is the first time you have been assessed a penalty.
