Forms 5498 & W-2 deferrals not matching

We have a situation where the deferrals per the W-2 is $5,200 but the 5498 only reflects $4,800. This has gone on for three years (2018, 209 & 2020). The payments were not monitored and we have a liability of $1,200. How do we go about correcting this? Should we go ahead and pay it even though it’s late?



The IRA custodian will only report on the 5498 contributions actually received by them in the calendar year. They may not receive the final paycheck contribution until January. Still, the 5498 should not be short consecutive years, because the late contribution from year 1 would be reported on the 5498 for year 2, and that would offset the final paycheck not being received. I don’t know why the same  400 shortfall would appear 3 straight years. 
The IRS has sent a tax due notice for 400 of taxable income for each year because 5200 was deducted and the 5498 was 400 short?

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