I think this is a bad diagnostic.  It only appears after the last Lacerte update, and never appeared in prior years.  The 1 on the first line is automatically populated when you do the batch efile of extensions, plus you WANT it to be there or else the invoice does not pick up charging for the extension prep.

Nonetheless, I think it is only a diagnostic for the efiling of the extension, not for the return itself.  Double check your ack file that the extension was accepted.  Then the filing of the return is a separate filing as the IRS already knows you have the extension so you are not refiling for it.  I would transmit even with the "critical" diagnostic, and hopefully someone at Lacerte is working on cleaning this up.