If the IRS is investigating, it probably WAS a 501(c)(3) but I wouldn't have any idea. I didn't write their application to the IRS. If they did, it is their own fault.
Any non-profit religious organization is automatically tax-exempt. The key is when they file with their state's Secretary of State, they need to file as a "non-profit religious corporation". This will also require a "Statement of Faith" and by-laws. The secret is to do it right the first time. No one offers this information, because it takes money away from lawyers and the IRS.
And that secret little 'loophole' previous known as the Constitution will soon be closed as people will accept the conventional wisdom that Churches are tax exempt solely because of some IRS codes.