When manually adding files to a custom list they are not obeying the sorting rules that are applied.
Example: I have a custom list labeled as "TV Series", this list has a filter set as "Blu-ray File | contains | TV Series , this list also has a filter set to sort by title ascending. Items that are automatically added to the list by the filter that is set are obeying the sort option that is set to sort alphabetically. If I then add items manually to this list they are placed below items found by the filter and are left in the order that I have added them.