Reproduction steps(video file attached):
1. Open the attached project.
2. Go to "Window > Sprite Packer".
3. Click "Pack".
4. Swap between "View atlas:": "HUD (Group 0)" and "HUD (Group 1)"

Actual behavior: 2 yellow stars are in a different atlas groups.
Expected behavior: both yellow stars are in the same RGBA atlas group.

Workaround:
5. Select "Assets > HUD > level_icon" asset in the project view.
6. Clear "Packing Tag" field.
7. Click "Apply".
8. Write "HUD" into the "Packinfg Tag" field.
9. Click "Apply".
10. Open the "Sprite Packer" again (step 2).
11. Click "Pack".

Reproduced with:
5.5.0b1, 2017.2.0a1