Just for the record or anyone else having this "bug" from Blender, I learned the issue. There is something called a "parent inverse": https://docs.blender.org/manual/en/latest/scene_layout/object/editing/parent.html So you have to be careful in Blender because you won't see this "hidden matrix" but if it gets created during your parenting (based on settings presumably I haven't figured out the nuance to yet), you cannot see it in your hierarchy or object panels. However, it does become evident on FBX export when it is applied. When I take the project with the bark object that keeps rotating -90 on export, if I click that bark (which shows 0 rotation at rest) and go Object > Apply > Parent Inverse, suddenly the -90 rotation becomes visible on the x axis. Then I can go Object > Apply > Rotation and now it is truly set to zero. Without doing the Apply Parent Inverse first, there is still a hidden rotation in there. So not exactly a bug. Just a strange design where they are hiding a potential rotation as the "Parent Inverse" rotation. If Blender was better designed, I think this would be visible on a panel somewhere instead of just hiding it completely. So if things are rotating weird, or you're not sure, Apply Parent Inverse to anything that is misbehaving then Apply Rotation.