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This problem still occasionally happens for me on the latest snapshot, but I figured out a way to fix this one my computer, not sure if it will work for others.
1. Switch texture pack to default.
2. Close and relaunch Minecraft.
I've been able to do this multiple times with success. I can even switch the texture pack back to a custom one after that and it will look fine.
If you switch to the default texture pack before exiting, you won't have to re-install like it says above or anything.