Wrong results may occur with discontinuous UVs, here is the way to fix it :
Step 1 : in this sample case we have a box with a atlas uv unwrap with will be projected to a sphere (the cube faces are pointing inwards)
If some points of the sphere already have uv values for the uvmap you want to edit, don't forget to clear the map for the sphere before running weighter, to start on a clean uvmap
Step 2 : Run weighter and select the UV map you want to use
Step 3 : As you can see, their are some errors
Step 4 : Select these polygons in the UV view and UNWELD (ctrl+u) them
Step 5 : Run weighter again and don't forget to select the UV map
Step 6 : Fixed !
Step 7 : You can now MERGE (m) the points unwelded in step 4