DFVC Filing - Overpayment of penalty

The plan sponsor failed to file the final/short form 5500 for the plan year ending 5/31/2016. We recommended DFVC, filed the return in November 2017 and paid the $2,000 penalty (this is a large plan) . The DOL's online calculator correctly indicates that the penalty is $2,000 (based on 313 days late).

The client received a letter from the DOL stating that they might have submitted an overpayment of $1,260 and included an ACH form for the plan sponsor to request the refund.  We called the DFVC number on the letter but got voicemail and have yet to receive a call back from them.

Any indications as to what might have triggered the letter? Anyone had any success in addressing this with the DOL? We don't want to overpay the penalty but we are pretty sure the penalty is $2,000 and not $740.

DOL may have subsequently calculated the penalty from 7/31/2017, the due date had it not been a short year, if the short plan year end wasn't picked up. I would continue to follow up with DOL and not file for the refund.

Agree with CuseFan, DOL is mistakenly treating this like a calendar 2016 return filed 74 days after the initial 7/31/2017 deadline.