QB Issue Resolution:

Look at the Item you used for billing. Make sure the expense side points to an expense account and the income side points to an income account (see insert).
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Resolution for Issue 'Why do my paid invoices show up in the ledger as payments that subtract from the total even though they are paid and deposited?' available: Yes (Solved).
Source: Intuit Community forum.

Why do my paid invoices show up in the ledger as payments that subtract from the total even though they are paid and deposited?: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

Support for Invoices
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Error Recovery for Invoices [Canada]
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