OBJ and FBX problems.

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Hello,
I have 2 problems with OBJ and FBX exports.
1. When importing FBX high en low poly in 3rd party software (Substance or Knald) 9/10 the high or low poly have a different location which makes it impossible to extract high poly data from low poly mesh. It also happens when using Xform and centering the pivot/axis.
When i models something in Max i export it as a OBJ to Headus UV Layout to unwrap and then import it back to Max. i think that gives some problems but cant figure it out..
2. When i want to bake my maps in OBJ instead of FBX with Substance or Knald, then the location is spot on, but.... i get small black artifacts/spots in my model..
Does anyone have a solution or similar problem? Please let me know because this drives me crazy.
Thank you!