Organizations that use Upgraded/Split Pledges will know that there is a Consolidated Pledge Schedule listed on each Pledge entry. If you have any Payments that have the same date within a Pledge segment, that extra payment will not appear in the Consolidated Pledge Schedule.
In addition to this, if your Pledge is set to Auto-process Payments the second Payment (that is dated the same) will charge correctly but a Payment will not be added to the Journal for that amount.
You will need to ensure you do not have any Payments with the same date. If needed, set them at least one day apart.