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Fixed in Unity 5.4.2
Some UV values get shifted by 1 pixel and results in incorrect UVs
Steps to reproduce:
1. Open attached project
2. Open scene "main"
3. Open Resources/Prefabs/Environments in project tab. Select HooverClassroom.prefab.
4. Right-click, and "choose HoodArt->swap crabby sprites". Each time you choose this, you should see the pencil case and part of the desk subtly shift up and down as this swaps between the original sprites and the sprites that CrabbyImporter is creating
5. Navigate to CompressedTextures/Environment/HooverClassroom_env
6. Select HooverClassroom_lookup.png
7. Right-click and choose "Reimport"
8. What you'll see in the console log is that for the original sprites, rect==textureRect in both cases, but for the new sprites, they aren't equal in the broken case. More specifically, the uv values match between the original and new sprites in the working case, and they're different in the broken case
Reproduced with: 5.3.6p3, 5.4.0p2
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