PTORock--What state are you in? In re-reading your post, I'm thinking that your issue is more one of exemption from state/local sales taxes than from corporate income taxes. If that's the case, my previous advice to talk to someone from the IRS isn't going to help you much. If you tell us what state you're in, then maybe some one else from your area would be more knowledgeable and could chime in.

I have filed for and received tax exemption for two different PTOs and I have never heard of a limitation on the number of fundraisers you can sponsor. That might be a rule of your district or local PTO folklore, but I don't think it's law. But there are other compelling reasons to consider both ways. In my opinion, if you are incorporated in your state, you have already taken a major step toward independence. But, you don't have to necessarily operate as an independent parent group, I suppose. We are incorporated and tax exempt, and we operate with our own bylaws and officers, so I describe us as "independent". But in fact everything we do is for the benefit of the kids at our school. Our independence lets us, the PTO members, to decide what activities to sponsor and how to raise money, where to spend it. But as long as our mission is consistent with the school's, it's a very blurry line between the PTO and the school, "independent" or not.

You should call the IRS and ask them, but I would think that you could still file for exemption and get it going back for quite some time, especially if you aren't a very big organization. You'll also need to check with whatever state you are in; they usually follow what the IRS does, but there's no guarantee.
If your receipts have been small enough so that you haven't been required to file a tax return, then there's really no harm in not filing for exemption earlier that I can think of.

Our PTO group has had a hard time trying to decide if we should be a part of our school system or become our own independent group. It was decided to become an independent group and then issues came up again so we went back and forth too long and missed the deadline for filing for tax exempt status. We created a company and became incorporated and that was as far as we got. One of our issues for becoming our own company was that three schools an elementary, middle and high school are all on the the school tax id number and if I understand it right we are allowed only two sales tax exempt fund raisers a year and our PTO group would get neither of these. This would hurt our fund raising quite a bit because the two fundraisers would be shared by so many groups. Being under the school system would make things easier but less profitable for our individual school. I find myself wondering if there are only a few hard workers so far in our group would someone be willing to take on changing the officers and the paperwork involved each school year. If we want to continue on and make our group tax exempt what options do we have now? Do we have to close the company and start over? Thank you for any suggestions!