There are a number of odd settings in MLS you probably need to replicate. Under "history", "automatically add history" is unchecked (presumably to allow the manipulations elsewhere). Under "other stage rules" there's all kinds of fate actions telling it how to assign the winners for the sub-comps. And specifically within the MLS Cup final stage, there's a fate action telling it to assign "team placing in competition" to "0" (same thing in the Western and Eastern Conference finals, which is required to clear up the winner there along with the stage finished action), that's referring to the sub-comp (i.e. the MLS Cup) which occupies that stage.
Also under the cup final stage, under "general" there's a couple of boxes checked: