We have the same problem with trust clients set up for electronic payment.  I discovered that it was only for trusts returns that were filed and accepted by IRS on March 15th.  Returns filed on all other dates are fine.

I have called the IRS and the also the US Treasury Financial Agent.  It looks like the payments (both balance due and 1Q estimated pmt) were never set up for processing.  The state payment went through fine.  I am on the phone with Lacerte trying to get more information.