Tree isn't object you have issues with. It isn't even WMO. You need to select every single WMO which was spawned by using 1.2 and middle-click while it is being selected. Without doing so, WMO data will remain corrupted a little bit. So, like I said, select your ratchet in SDL 1.3/1.4 and check if you can see big green box around it, I am not sure what is that box, some kind of bounding box of WMO? Whatever. If you can't see it/it is very small and just somewhere around model's origin, then you need to do that middle-click. Without that you fixed nothing.
In a short version - 1.3/1.4 SDL need to be used to spawn or move trouble-giving WMO model to fix that model's data, just saving ADT in that noggit version won't do anything on its own.