The way the report card works is that it first looks at the type of transcript definition that is attached to the transcript record and then it determines how many columns it can post. At the Cyber School when the courses were first set up the transcript definition used was "Rubric and Term Grades (4 Term)", this is also the Default Transcript Definition of this school. In a different ticket we had fixed this issue so that your courses are now using the "Rubric,Term, and Final Course Grades (4 Term)" transcript definition so that a Final Grade can be entered. 

Once a Transcript Record is created the name/type associated with it "sticks" even after it is changed on the course and then the grade input is re-prepared. As you can see in my screenshot, there are 389 Transcript Records that are still associated with the "Rubric and Term Grades (4 Term)" TD because these records were created before the change was made. You can also see that they do have Final Marks because of the change to the new TD "Rubric, Term, and Final Course Grades (4 Term)".

Now for these records, when the report card looks at them it reads "Rubric and Term Grades (4 Term)" and it determines that a Final Grade does not exist so we will not show it on the Report Card, regardless if there actually is a Final Grade in the Transcript Record.

Getting back to your original question, since the Transcript Definition on all your courses has been changed to "Rubric, Term, and Final Course Grades (4 Term)" before any transcript records were created, for the Semester 2 courses you should not have the same experiences as semester 1. As along as when the transcript record is created the name/type associated with the record has a field for Final Grade it will print on the report card. You should have no problems with the report card in Semester 2.