late 5500 filed, extension not recognized

We have a 401k plan with a 3/31 PYE.  We filed a 5558 before 10/31, completed the 5500, which was filed around 12/20.

However, the IRS sent a letter stating that the 5558 was received late and therefore was rejected.  The 5558 was not mailed with tracking and not filed electronically.

Just curious as to whether the plan sponsor has any options here.  They already filed, apparently late, but that has not yet been "caught" or addressed by the IRS.  Can they file via DFVCP, pay the fine, and put this behind them?  But is DFVCP available if they are already filed?  

Thanks for any replies

I have received two letters this week, both for 12/31 plan year ends.  Extensions and 5500s filed timely.  The letters both had an incorrect tax period.  I'm curious if yours is correct on your letter?  I'm thinking this is a glitch on the IRS's end.  That said, I usually just lay out the facts with dates in a response and pray I hear nothing in return.

The information in the letter is all correct. 

DFVC is still available until you get a notice of Penalty letter from the DOL. Then DFVC is no longer an option.

Even a notice and penalty from the IRS does not disqualify a plan from filing under DFVC, as long as they pay the  amnesty fee.     We always send the 5558's using certified mail, return receipt requested....just in case.  However, consider that the government shut down may have resulted in LOTS of unopened envelopes at the IRS.