This may occur if the School is marked incorrectly for the Transfer Courses. 

To update the status of the Transfer school for a student: 
  1. Within Education Edge, navigate to Records
  2. Click Students
  3. Open student record
  4. Select the Education Tab
  5. Highlight the school that the transfer course is missing from 
  6. Click Open
  7. Update the field 'Education type:'
  8. Click OK
  9. Click Save and Close

Once the School has been updated, run the transcript again to display the transfer courses on the transcript. If the transfer courses are still missing from the transcript, please refer to Transfer courses for one organization do not print on transcript for further troubleshooting.