Well, enabling the map on the second layer and running Auto on Texture Buddy did the trick. But if you build the map with Auto UV Map on (and without clicking on Auto like I did), the problem still persist. As far as I know, the final map only had one UVMap, just like every sector and brush. In the meantime, I can live with it. It's just something that started happening after I reinstalled Blender and the Level Buddy tool.
And I must say, it's being incredible useful once you get the hang of it. With automatic UV and exporting, it let me modify the map and send to Unity in a matter of few seconds!
