it is not an adjustment to your tax liability. so for purposes of avoiding an underpayment penalty you ignore the refund and look at your tax liability excluding the penalty.
there have been many threads about the IRS and Turbotax computing different amounts for the underpayment penalties - even 100% differences - and I don't think anyone knows why this is occurring. If I had to guess at one possibility it would be that at least some of these taxpayers qualified for natural disaster relief and could pay their estimates later than normal but Turbotax doesn't know or programmed this.
