Talk to the management, and reinforce that you are a regular customer... could they please investigate,
THEN....
call the company on the box, and explain. Ask if they treat the stock in a way that could damage the goods... OR is it something that happens after they shipped it to XXXXX (store name).
Tell both parties you have spent a great deal of money on the product, and an upper echelon company like them should take care of regular customers.
THEN, leave a comment on the trader joe page on Facebook.
Write them a private message on facebook, and finally write to corporate headquarters.
Your name will get around fast, and they will compensate you for the broken ones, and after blaming each other, they will fix the situation.
Personally I use Kroger Graham Crackers (Fry's).
I use the Honey graham, but all are good. Never a broken one.
I know you want natural......
the solution above will get some sort of action.
Otherwise you may have to change.
I wish you great success.