Looking carefully in the manual (under merging virtices though) i found what I was looking for:
"Edges will not merge if the normals of adjacent faces point in opposite directions. Try either of the following before performing the merge:
Select either of the adjacent faces and reverse the normals using the Reverse and Propagate mode. For details, see Reversing polygonal normals.
Merge the vertices, which will make the object nonmanifold. Perform a Cleanup on the object to remove the nonmanifold geometry and conform the normals. For details, see Cleaning up polygonal data."
I reversed the normals and everything went smooth as a babyass.