Payroll just withholds according to the W4 that you submit to them. If that W4 isn't set to withhold enough, then you won't have enough withheld. So payroll is likely correct in telling you they did everything right. And your CPA is likely also correct....you didn't have enough withheld, so you owe.

That being said, I really don't know why your CPA will need to go through each of your paychecks. All they need to know is your final income numbers, and how much in total was withheld.