If she retains ownership, I wouldn't fight the parent for any interest in it with regard to future sales proceeds. I would expect the right to continue to use the program free of charge since the parent did volunteer his/her time on committee to develop it for the school's use to begin with. If the PTO had known there would be a charge for use at some point down the road, you may have gone a different route or may have looked into buying a program from a bonifide vendor to begin with. Plus, I imagine multiple people gave of their time and effort to "debug" it and load data into it for the PTO's use. Most developers consider beta test sites like your PTO to have provided a lot of value in the development of a successful program.
Other than that, I wouldn't worry about the situation. Any proceeds that the parent chooses to give the PTO won't negatively affect its non-profit status.
I see no issue with it from a non-profit perspective. Lots of non-profits sell goods or services. The only issues I can see is regarding the ownership of the program. I take it that the parent is giving ownership of the program in the application for copyright program to your PTO and that all proceeds from future sales will wholly belong to your organization? Will any future upgrades also belong to your PTO since the copyright of the base program's ownership belongs to your PTO?
We have a parent who has developed a program through a PTO committee. She is going to copyright it and try to market it. Does this in anyway effect our non-for profit status? Can you see any other issues that could adversly effect our PTO?