My allegation was that the IRS chose to be stricter with X.org than it is with other nonprofits.
3 years of silence and then a sudden tax exempt revoke is a very cagey response to 3 years of not filing any tax returns.
The IRS shouldn't have waited that long without sending notice.
The fact that the feds and the corporations are in bed elsewhere is also a good reason to at least suspect underhandedness on the IRS's part.
Actually, that's pretty normal for the IRS. The IRS is not, actually, much in the habit of giving warnings. It takes them a while to get around to things, and once they do, its pay-up-or-else (or revocation or whatever). They aren't well enough funded to bother with warning notices, or hearings, etc. If you disagree with their finding, there are things one can do and an appeals process, but generally they don't initiate such things except in certain categories of audit issues.