Customers can be set to an "Application Method" of "Apply-to Oldest". When this is set and a Cash Receipt Journal is posted the payment is applied to the oldest transactions first and just gets applied until the Payment is exhausted.
The Bank Recon. Journal does not follow this convention on automatic application and attempts to apply to the newest outstanding entry with that amount, otherwise it just applies as much as it can to the newest invoice, not the oldest invoices as should it should be because of the setup.
When using Automatic Application in the Bank Recon. Journal the Customer Card setting for "Application Method" needs to respect the setup and not just ignore it.