The AP-I and AP-F programs use different logic.  AP-F looks at the AMTRM field (amount remaining) in BKAPNIVT (invoice file) while AP-I starts with the original amount in BKAPINVT and then subtracts based on payments in BKAPCHKH (payment file) up through the "as of" date of the aging.  Sounds like you have BKAPCHKH records that aren't linking right with the original invoices, causing paid invoices to show on the aging with a balance due even though the amount remaining is actually 0.  Take a look at both files in Maintain Database, email me if you need help sorting it out.