Thank you, 

I just checked the W-2 again. Box 12a is "S 1649.96". Retirement Plan box is checked in section 13. I'm wondering where the 3401.44 comes from? Maybe that is the error the IRS said that it corrected with the employer? The message was "We didn't allow the amount claimed in a deduction for self employed SEP, SIMPLE, and qualified plans on your tax return. Your employer has already adjusted Box 1 of your Form W-2 to exclude this amount. (1610) 

I put into the system exactly what was on the W-2 AND the Form 5498.  Because the figures didn't match, I thought it was two separate deposits. However, I am definitely happy to make right with the client.

Thank you for taking the time to respond!

Dawn