Posts which you have never marked as paid show up as already paid, making the author balance incorrect (or even negative).
This problem probably happens because you use a duplicate post plugin: when you duplicate a post, depending on your settings, even the post custom fields could be copied. Post Pay Counter payment history is stored in a (hidden from editor) custom field, so that if you duplicate a post, even the payment history gets copied.
To prevent this, you need to edit the duplicate post plugin settings, adding to the fields exclusion list _ppcp_payment_history. In the following screenshot you see how Duplicate Post should be set up (look at the bottom field, under Do not copy these fields).