On second thought, you might have luck reviewing the Credits associated to each course period.
Here is the help:
Credits is both the coefficient used to weigh Final Grades in order to calculate the overall / cumulative GPA, and the Credits attempted by students. 0 credits will be earned by a student whose grade is below the minimum (see the "Minimum Passing Grade" field in the Grades > Grading Scales program for configuration). Credits earned can be displayed on Transcripts and Credits can be displayed on Report Cards. For example, if you assign 4 credits to a Full Year Course Period and have 4 Quarters, students will earn 1 credit for each Quarter.
Your issue might be a credit issue.
For example, if you have course A with 2 credits.
And course B with 1 credit.
The cumulative GPA calculation will weigh course A twice as much as course B.