I am still unable to reproduce this with Max 2013.
When you say “Clone” your mesh, are you doing a copy, instance, or reference to the one it was “cloned” from? I’ve tried with copy and instance with everything working as intended.
There has to be a step that is being assumed here and not mentioned that is leading to this behavior. 
Would you mind detailing all your steps from Max to UE4 to get the error. I don’t have access to Max 2015 and the guy on our support team that has it on his machine is out this week. So just to narrow down the other steps first would be good to know.
Here are my steps:
- Created a cylinder with some extruded faces to easily tell which part is where
- tried a copy and a instance of the mesh (separate tests)
- Exported both the original and the “clone” in the same FBX
- Imported into UE4 (Tested with combined and with combined unchecked)
These are my steps. I didn’t get have any issue with this at all.
Here is the FBX and the Max file I used if you’d like to test as well.
Thank you!
Tim