It just came to my attention that my accountant never e-filed/submitted my companies 2012 1120S. It was rushed into a local IRS assistance office exactly 7 weeks ago for submission.

As of today they mentioned over phone support that the return was rejected but didn't have an error code and showed that they had everything they needed/its still processing.

Will this effect the 6-8 week processing window (delay?) and will the return still process and post to my transcripts

As of last friday it just had a status of received/processing