Do you have retained samples from your production run? Did they have mould?
It seems odd to have mould on cookies. Unless the moisture content was really high.
I suppose there are a few possibilities and what I'd do is get a team together to brainstorm potential causes. Things I'd think about would be:
- High moisture at manufacturing (accuracy of measurement?)
- Hygroscopic product absorbing moisture during life (damage to packaging? Dryness of gas flushing process?)
- Moisture trapped within the packaging (I've seen this in bread packaging before when it was packed hot.)
- Spores in the environment?
- Anything in the recipe which could be breaking down or crystallising so that you get moisture being "freed up" from solutes?
- Potential the accelerated shelf life process wasn't designed to accurately replicate reality (albeit if the moisture were low enough that shouldn't be an issue.)
Do you have a US equivalent to Campden BRI? I.e. a research organisation? Not that Campden are as good as they were but you just know there would be a cookie (biscuit in UK English) expert there who you could talk to. Although if you're gas flushing these, if that is to control moisture it does suggest you might have been on the raggedy edge of what's possible.
Another thing a more expert person than me could wade in on... For bacteria I'd definitely be interested in water activity but water activity and total moisture are not the same thing. Aw is heavily impacted by solutes. It would be really interesting to do some total moisture testing on your product. Because I have a gut feel that could be quite important.