I know this is an old qustion, but I've encountered the similar case so leave a reply here :
In my case, we needed to use a separate uv channel for normal on a character cloth.
The model was exported from the 3ds Max. And it had no problem until our 3d artist done a skinning job.
It turned out that the modifier stack order can cause this issue.
You should order the modifier stack so that 'Skin' modifier is on top of any 'UVW Unwrap' modifier.
Hope this helps someone in future.
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