I've had the IRS take over a year to approve an S election.  We then get an e-file entity mismatch on an extension or on the filing of a return.  Confirm the S election was actually sent, then either delay the e-file, or mail in the return with a copy of the S election (or late S election) and a note about it.  

Ive seen others mention this over in the FB tax pro groups, do you have it marked as Initial return?

I had one on the 15th in it's 2nd year with a mismatch so Initial Return may not be the answer.

where can I check as initial return