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I also noticed it with houdini and a variety of other 3rd Party software - i'm not talking subtle differences either, it was pretty extreme. That's how I discovered the differences to begin with. The best way to see if this is the same as your issue would be to experiment and see what comes out of it. and the way the older versions import compared the the latest version is night and day.
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the latest version of lightwave has an updated fbx import. The reason I made that comment was because I saw a similar error with lightwave.
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