I take it you are using a version prior to 2007.
When you run your ageing report by journal entries, B1 will show you the full amount as due for all partially paid invoices & also, in another row, the actual partial payment. This is due to the 2 different reconciliation engines. You need to manually reconcile the invoices with the partial payments, then they will no longer appear in the ageing by journal entry.
To determine which payments belong to which invoice, you could run the report by marketing documents. There B1 will show you the remaining outstanding amounts only, from which you can deduct the payment(s) & thence reconcile the correct documents.
As a rule, SAP recommends to only run the ageing reports by journal entry.
If you are looking for more info on reconciliation, please have a look at the IRU landing page:
All the best,