ANSWER: The best practice would be for the check to come to the PTA and for the PTA to grant the money to the school. In this kind of transaction, the budget most likely would have a revenue line item that matches the expense line item. In this case, those line items would show as zero and a footnote should state the dollar amount received, that the school inadvertently cashed the check.
If the school used the money towards the same thing the PTA is granting funds for then they should deduct that amount from the total they had budgeted to grant to the school. If there were additional monies budgeted to be granted to the school, in addition to the box tops money, the PTA should go ahead and grant the additional money to the school so that they maintain compliance with their budget. If the school used that money towards something else then they will need to make the decision about whether or not they will still grant the full amount. Depending on the amount and how far out of the approved budget it may need to be taken to the general membership.
I highly suggest that all PTAs, but especially those that participate in programs that send checks back to the PTA (Box Tops, Matching Funds, etc.), rent a postal box. Having a dedicated address that is separate from the school would alleviate this type of problem. This also helps for where to send bank statements, where people can send membership payments, etc.