My experience is that AC gets confused about libraries on a server, when the parts are opened via the Open dialog, as opposed to selecting an object and doing Cmd+Opt+O.
Libraries on local machine: Always OK.
Libraries on server, opened via selection: OK.
Libraries on server, loaded parts opened via dialog: "Same name" warning, followed by placement in Other Parts and duplicate report.
In other words, AC doesn't realize that the path in the Open dialog is the same as the loaded libraries path, when that path is on a server. Bug.
As long as you are sure you are saving on the correct path, all you have to do is delete the redundant items under Other Objects. Or, place an instance of the object and open it from there.