You can fix this in one day. Take the first step to becoming independent of the school district by calling the IRS and getting a new tax id number for your PTO. Before you call, go to
Internal Revenue Service
and look up Form SS-4. That's the instructions for applying for a new tax id number. The IRS will assign you one right over the phone, no cost. Then go to the best bank in your area (not necessarily the same one you've been using, this is a good time to look for the best services, lowest fees, and proximity) and open a new small business checking account with the new tax id number. You might need a minimum deposit to open the account, so you'll either need to get the district to release some of your money, or you can make a personal donation to the new group, or I suppose you could loan the group some money, but document it all very neatly so no one can question your motives later. Once you have a tax id number and a bank account, ask the district to cut your new PTO a check for the full amount of your balance.
I learned in a PTOToday conference years ago that if your money was held in a school bank account, the school could legally seize it, but yours if the first real life example I've heard of. I hope it all works out for you, but you bring up a very valuable lesson for other PTO's who just assume their tax id number is their own.
FOLKS: check your bank account. If you are not 100% certain that you are banking under a tax id number actually tied to your PTO, go find out for sure. If you are banking with the school's tax id number, get your own tax id number before your funds are frozen like smmorris's. (ok, there are some groups who knowingly and appropriately bank under the district's control, but that's a special situation and one that I would not describe as an independent parent group. That's more like being a committee of the school).