Payments not applied after remote call to quickpost

We have some custom code in our system with remote calls to SFPQKDRV (quick post). It works just fine so I'm trying to use the same approach now to create another tool that will automate a very time consuming process.

The process is posting charges to balance over-payments. So for example, a $40 payment will exist that is not applied to anything. The process looks for such payments based on some specific criteria, inserts a $40 charge into quick_post_tbl and then remote calls SFPQKDRV. The charges always get inserted successfully by this process into the item_sf table.

The issue is that it doesn't seem to always trigger the payment applier. On simple tests with a single row of data it works just fine, but as soon as there's more data to post, most of the payments don't get applied to the new charges. If I manually apply them through "Apply Payment" for each common_id, then it works, but I need to make sure this part is automated as well. Is there something I can do to make sure the payment get applied? Or is there a way to manually call the process which applies