The IRS can take much longer than the posted time frame to process that information ... I would not be surprised that it took much longer or they sent you another notice for an additional 60/90 days to process it... all you can do is be patient.
This is nothing you or the program did wrong ... the IRS may not have gotten the info from the employer to verify what you put on your return thus they asked you for it or it could simply be a random audit.
