Can you describe what is or is not happening?
It's kind of a weird tool. When you engage the tool it will show you the highlighted eges between what was in this case seperate patches. When you engage the merge edges tool it will turn an unmerged edge piunk when you click on it. Then when you click on an edge it will turn tan then when you click again it merges and will no lionger highlight that edge when you click on it. In otehrcases when you click an edge it will create a flag that indicates the othe rpossible edge to merge to and you click on it then it merges them.
Obviouskly a succesful merged egde will not seperate when you move the face.. to test you result create a nurbs cube and covert it to polys. Now select all the faces and merge them. Then try using the merge tool and then try move one of the faces that was merged and watch how the edge reacts. If thhe pafce still pulls away then you are doing something wrong.