OFB-12

In our case, a 3-1-0 point system was used.
First question: how many points should be awarded for an unplayed game? As we found out, the program awards 0.5. Ideally, it should be 1 – like for a draw. But what is the correct approach?

The correct approach is what you would do manually if there were no program.
If you (as the tournament judge) believe that 1 is the correct score for an unplayed game, then that is the correct approach.

Therefore, the program is not doing what you want, so as a programmer and a user, I'm telling you to discard the program and calculate everything manually, as you believe it should be done.
Close the issue that is currently at hand.
Then, deal with the program, or find a new one, so that you don't step on the same rake next time.

P.S. Another option is that maybe you can trick the stupid program. If it rigidly assigns 0.5 to unplayed games and this cannot be fixed.
Then maybe you can set 1.5 for a win and 0.5 for a draw.
And then it will calculate everything correctly on its own, just on a smaller scale (twice as small).