Currently if you have the Course set in
  1. Core
  2. School
  3. Departments and Courses
  4. Search the Course Name and click the editing pencil
  5. Click the Grading Tab and 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 a existing Enhancement Request to get them to match, you can see and vote for the Idea here: