I find that I have to save the scene when editing prefabs with FMS's to have some changes take effect at times (No reason/pattern I can detect except it only seems to take effect on "older" prefabs, ones that have been reworked/edited a few times). I have a habit of always Ctl-S'ing before running my games to make sure changes take effect. I find that the actions with XML Datamaker are notorious for not having their prefab values keep unless I save after changing.