i have a server with plots in a town that are for sale. I have one diamond block in each and used drawing mode so it only protected that plot. everytime i restart my server there is one or two fields that are reset to the default size. when i restart server i make sure to save it so it is being saved. The plugin i am using to save is World Saver.

Try it again, this time force a manual saving of the fields to the database with /ps save. Then check your database and see if the new dimensions got saved or not. Let me know where it breaks down.