Form 5330 filed electronically late with an excise tax due

We use FT Williams.  We tried to help a client file a 5330 to pay the excise tax for an over contribution.   FT Williams tells us the filing rejected because the form was late and money was due.  They however don't give us any insight how to get the payment and filing done in the correct order. 

If anyone has done this successfully we could use some insights on how to do this. 

This was so much easier with the old paper forms.