I'm brand new to this, (I just joined our PTO and have only been to one meeting so far) but appreciate your question and will watch for answers because of what our PTO is currently going through:
After maintaining a PTO bank account with safeguards for several years (with no problems and all funds/receipts accounted for) our School District suddenly demanded that our PTO turn over our bank account and balance to them. They withdrew the money and closed the PTO's account. They said that they were required by the state of Colorado to keep all PTO money in their account as a line item under our School's Activity Fund to protect against fraud, theft, & liability issues. (I can see their point on this, because our PTO was using their tax ID# at the time, and didn't have one of their own, nor did they have their own insurance.) Now if the PTO wishes to access any of their money, they need to provide a written requisition to the school and be approved by the secretary before they can access their money.
Some PTO members are upset about this, and would like to have a separate bank account, (again set-up with safeguards), their own tax ID# and their own insurance. This alternative has seemed to infuriate the school, and they are insisting that the State of Colorado will not allow this, but we are not finding any evidence to support that claim.
I have also been told that at the last PTO meeting before this, only 2 parents were in attendance (compared to many teachers and administrators) and the Principal made a motion requiring the PTO to pay the School $500 per semester to be used at the principals discretion. The motion was passed.
Now the PTO has very little funds left. They are currently holding a fund raiser and have committed the money they will raise to playground improvements. (which will cost $2,000) However, they may not be able to fulfill that commitment due to the $500 obligation. When asked what would happen if they didn't have enough money in their account and couldn't pay the $500, the secretary said it would go into arrears and be owed. Does this mean that the members of the PTO are liable for this debt? Can it be legally collected upon? Is it legal for a school to set an ongoing payment obligation for a PTO in the first place?
I don't know what to think about all of this and am having a hard time getting straight answers. In a way it is a similar situation to your stealing situation. Should a school also have internal safeguards in place to protect the use of PTO money...especially if the school is controlling the PTO (by majority) and the PTO's money (by housing the account) and can elect to not have to disclose how the money was spent?
These are just a few of my questions, and I don't have all the facts I'm sure. However, I would think that if your School District wants to audit your PTO's old account you should count your blessings! You reported the missing money to them and they may help you discover where it went, when it went; and give you a chance to bond together in the quest for an honest and cooperative financial relationship. Too bad they didn't have your back when you needed them and it wasn't convenient (or legal?) for them to get involved, but maybe this will help you all make better arrangements for a future PTO. OR...perhaps they have recently discovered that they WERE liable for the PTO's account and DID have a responsibility...I would ask them this (again). That is what our School District is saying...that they were liable for anything that could happen to the PTO funds, and so our PTO MUST be "under their umbrella" for liability reasons, and therefore they must manage our account. (But if you had had your own tax ID number, and insurance, the case may have been different and they would not have been liable, but I don't know the answer to that yet...)
Something to think about anyway, and it didn't look like anyone else had responded to you so I thought that I would!