Generally, an organization applying to the IRS for recognition of 501(c)(3) status retroactive to the date of its formation must file a properly completed and executed (signed) Form 1023 within 27 months after the end of the month in which it was formed. So, an organization formed on January 15, 2011 would have until April 30, 2013 in order to meet the 27-month deadline. If the organization files Form 1023 after the deadline has passed, generally, recognition of 501(c)(3) status will be given only from the date the Form was filed.
For many organizations applying to the IRS for recognition of tax-exempt status under sections other than 501(c)(3), the appropriate form to file is Form 1024. Before 2013, the 27-month deadline applicable to 501(c)(3) applicants did not apply to these other organizations because they were never strictly required to apply for recognition of tax-exempt status in order to gain the benefits of tax-exemption under sections such as 501(c)(4) (social welfare organizations), 501(c)(6) (business leagues), and 501(c)(7) (social clubs). If such organizations wanted the benefits of a formal IRS determination, they could file Form 1024 at anytime, and generally, the IRS would provide a determination letter recognizing exemption retroactively to the date of formation so long as the organization had always met the applicable requirements. For example, a 501(c)(4) organization formed in 1981 could have filed a Form 1024 in 2012 and received recognition of tax-exemption retroactive to 1981. But this IRS practice changed on January 1, 2013.
In Rev. Proc. 2013-9, the revenue procedure setting forth procedures for issuing determination letters and rulings on the exempt status of certain organizations, the same 27-month deadline applicable to 501(c)(3) organizations is made applicable to certain other exempt organizations. Accordingly, the 501(c)(4) organization formed in 1981 could now only apply for recognition of 501(c)(4) status from the date of its application to the IRS. This doesn't necessarily mean that it wasn't tax-exempt from the date of its formation, but it simply doesn't have the benefit of the retroactive IRS recognition of tax-exempt status. Practically, this might be a problem if the organization had not been in consistent compliance with all of the requirements under 501(c)(4). On audit, the IRS could say it was never tax-exempt and hold the organization responsible for past due taxes, interest and penalties.
See also this Proskauer Rose article on the change.