Not sure if it's me or a bug...
1. Create sprite collection.
2. Drag cloud1 into Texture Refs.
3. Commit.
4. Click on the button to the left of Element 0 and select crate from the list.
5. Click Commit.
6. Create a new scene and create a sprite.
7. In the Sprite drop-down list, the crate is called "cloud1"
My workaround: return to sprite collection, set Element 0 to nothing, commit, set Element 0 to crate, commit.