I had this happen with the first 4 federal returns I filed where the client owed federal tax and was having it electronically withdrawn, but box 5 is checked. I haven't called the IRS yet. I have been on Proseries phone hold for just over an hour now. Every time I called today, it said the wait would be over an hour.
What happened last time? Did your client payments to the IRS ultimately go through despite box 5 being checked?