Currently, if you have the Course set in
  • Core
  • School
  • Departments and Courses
  1. Search the Course Name and click the editing pencil
  2. Click the Grading Tab
If the  "How should this course appear on transcripts ?"Abbreviation: is being used then the Course will display on the Transcript as the Abbreviation and the Courses in Progress will have the actual Course Titles

For example:

If in Core you have the Abbreviation as  AP-BC Calc but  Calculus II AP on the Course Title then it will display as 
Calculus II AP on the Courses in Progress and AP-BC Calc where the Course Title is for the Grades that have been recorded.
User-added image
There is an existing Enhancement Request to have them automatically match, you can see and vote for the Idea here: