I think I found the issue with item #2. There's an option to combine games with the same titles, so that you wouldn't get 3 separate entries for a game that has a RevA, RevB, etc. However, the import seems to be skipping the first game when there are sequels.
For example, it skips "Adventures of Lolo" but imports "Adventures of Lolo 2" and "Adventures of Lolo 3". This is why I did not get TMNT1 imported, but got TMNT2 and 3 imported.
Is there a setting that prevents this?