The only time I've seen the behavior you're describing is when an element already exists with the same Find Logic, but with a different name. Typically if elements are truly duplicates (on the same page, with the same find attributes) Test Studio will not add the new element as a duplicate. It will record the new test step and reference the already existing element.
In order to investigate what is causing the issue we need to be able to reproduce it locally in our source code debugging environment. Please send us a copy of your WPF app or ask you developers to put together a small sample WPF app that has these controls and send it to us(in a .zip file). Keep in mind that we are communicating in a forum thread which is public and if you are willing to provide any sensitive information you should open a support ticket where all the information remains private and confidential.