QB Issue Resolution:

Do you receive the payments via check? Credit card? How are they recorded in QB?

Only things that look like cash or check payments will appear on the 1099’s. Things like credit card, PayPal, or ACH/DD transactions (essentially anything electronic and not paper) no longer appear on the 1099 Misc form.

Resolution for Issue 'quickbooks 2014 not including all payments for a 1099 vendor' available: Yes (Solved).
Source: Intuit Community forum.

quickbooks 2014 not including all payments for a 1099 vendor: 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 1099
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Error Recovery for 1099 [Canada]
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