What folder are you opening with ZOOT? Be sure you are opening the folder right outside the object or scenery or animals etc folder.
If you mean the black dots next to each name - I usually have that happen when I open the wrong directory (example I go to far into my creation and open ... maybe the objects folder instead of the folder outside it).
Here is what your creation looks like:
For Scenery:
Name
- Scenery
-- Other
- Objects
For Animals:
Name
- animals
-- etc
ZOOT can open buildings and other types as well, but the point is to open the folder in the example above "Name", not any deeper or any farther out.