Your scenario sounds a little bit from your description, but I've often seen a similar thing happen when zero dollar payments occur. I.e. there's a Bill and a Credit/JE sitting out there for the same amount. When those are "paid" through Pay Bills, it simply marries those two up and marks the Bill as Paid and the Credit/JE as applied, but NetSuite doesn't actually generate a zero-dollar Bill Payment record. Thus there's nothing actually keeping those two records connected, so when the Bill or Credit or JE is updated (even via a script or something that has nothing to do with payment application), it automatically unapplies it and then both the Bill and Credit/JE are sitting out there again waiting to be applied to each other again.