In the PGN window, when there is a comment before move 1, it is not displayed. When a comment is added after move 1, that comment is displayed both before and after move 1. Removing the comment before move 1, then only the correct comment after move 1 is displayed. It appears that the logic checks if there is a comment before move 1, and if there is, it displays the comment after move 1. This is Scid 5.0.2 on Linux.
Fixed with:
https://sourceforge.net/p/scid/code/ci/e663449dc117dcae66899f13ab6ccb918e6e95fa/