Problem with Texture Atlas

So I've been trying to import a character into Unity.
For some reasons I had to create only one texture image and to do that I used Texture Atlas. Everything was great till I imported the character in the scene and I realised that my UV got messed up.
This is what I got
Do you guys know what might cause this?
And no... I don't have the interactive licence. I am going to buy it only if I'm sure that I'll manage to make the game work.
Comments
What are you exporting as? If it's an OBJ export, perhaps try collapsing the UV tiles?
I export as FBX..