I would need to see your specific case to comment on the rankings of particular trinkets. The easiest way to do that is to provide a snapshot ID, which can be generated via the “help” link next to any section header – the following post has detailed instructions on how to do that:
Once I see your case, we can see if there is a particular setting causing the optimizer to make its choices, talent combination, etc.
Generally speaking without seeing the specifics: while some trinkets are certainly more powerful than others, unless you are using the absolute worst trinkets instead of the absolute best, it won’t change your in-game performance by that much. In other words, you won’t all of a sudden start ranking really high just by changing your trinkets. People tend to fixate on them because they are the most unique items that you equip, but they aren’t any more powerful than say your helmet or leg item.