Link the gradebooks to all of the report cards needed.
  1. Under the homeroom group, click Report Card under the Quicklinks
  2. Click the Report Card button 
  3. Click View next to the subject
  4. Click the link that shows what gradebooks are currently linked
  5. Select the gradebook to link from the popup window
  6. Click Add
  7. Click Apply to All Fields 
  8. Click Done 
  9. Repeat for all report cards, as needed
Now the gradebooks are pulling from the correct academic subgroups, and the report cards are pulling all gradebook data.