I have a similar problem with a different twist.  Doing a 990 for a Masonic organization.  They had been incorrectly using 501(c)(8) code, which is for a fraternal benefit society such as Woodmen of the World (basically an insurance organization set up under a fraternal umbrella).  In 1969, Congress established/created the 501(c)(10) to differentiate the organizations that do insurance vs those that don't.  Most masonic organizations are 10's, as they aren't in the life/health insurance business.  So, I put 10 in the place designated for the organization type, and the e-file is rejected because of it.  Putting an 8 on the form would be knowingly incorrect, which is not a good way to conduct business.  IRS now requires e-file for 990's; how do I get the matter resolved?