So my clients just emailed me a copy of the notice IRS sent the wife.

The good news is that it shows the same AGI, taxable income and withholding credits as those reported on her superseding return.

The bad news is that it doesn't show her half of the single $8,500 ES payment that had been made jointly in September.  As a result, she is being billed for !,500 plus interest and FTP penalty, rather than receiving a refund of $2,750 plus interest.  (Each return claimed half the ES payment.)

The good news is that for the husband, "Where's My Refund" is accessible using the refund amount shown on his superseding return. 

The bad news is that his return is still being processed.

I told them to wait a few weeks and hope the husband's refund shows up, including all of the ES payment and not just half of it.  

They're smart enough to set up an online account, so we might try further research that way.