The IRS has "misplaced" a ton of 2553 forms in the past few years.  Also, acknowlegements can take well over a year to process.  It has caused me many nightmare issues.  My suggestion is to read the Late Election section of the 2553 instructions and submit it again (initial return or amended return) with an explanation.  Since this has to filed via a paper return it could take more years to hear back.  Very, very frustrating.