If an invoice appears on the Non-Exported Invoice report but is not part of the export file (does not get imported) it means there is invoice information that is not properly linked to either the chart of accounts or tax rate.
Check revenue codes associated with the invoice items to make sure they are in the Chart of Accounts for the branch. Sometimes if a new branch is added they forget to setup the chart of accounts for that branch.
Make sure that the Tax Code on the Job is valid. TCR Support may need to check the GroupTaxID field on the job to make sure it is valid.