I don't think that's the issue. I think it is more of a case of whether or not the corporation and the foundation really are two separate organizations. Until the new director of the foundation arrived (Mark Surman), the foundation didn't really appear to do anything. To the IRS, this may have looked like the foundation was only a tax shelter for the corporation and not a real thing.

Now there's all this Drumbeat Festival stuff, etc.. coming out the foundation. Clearly they are trying to position themselves as a non-profit that advocates for the open web rather than just a company that gives away a browser. Owning a corporation that gives away a browser is just part of that cause. Hopefully that's how the IRS sees it.

Sadly, I don't think a lot of the foundation sponsored stuff really ever links up with anything happening on the corporate side. At least from the outside, it still looks like the corporation wags the foundation and not the other way around.

Edit: Yes, the foundation does own the corporation.