Removing a group doesn't remove joints.
When you merge 2 models, the resulting one get 2 "skeletons".
You will have to delete the second skeleton (which come from the merged model).
This is a tiresome task because you must not only delete joints, you have to tie vertex from the merged model to the first skeleton.
In Joints thumbmail you'll have to select "SelAssigned" vertex for each joint, then "Show" vertex weight, "Select", tie selected vertex to the good joint and repeat the process untill you receive "Please select the vertices you want to show in the weight editor" (it means you have no vertex tied to the selected joint).
This process begin with the last joint (joints list bottom), and you will have to repeat the process for each joint until you have only one skeleton.
Do not forget the "SelUnAssigned" vertex at the end, you will see if some vertex are not tied to joints.
I hope it's not too unclear...
