It sounds like you are trying to open your figure files from outside of MATLAB (e.g. Windows Explorer), and it is pulling up a new instance instead of opening inside the already-open instance of MATLAB. This sounds similar to an issue detail here (about ".m" files).
Also, make sure that you have your system set up to open ".fig" files in your newly-installed version of MATLAB, not any old version you may still have installed.
If you can't get anything else working, you should be able to the ".fig" files from within MATLAB, and I would expect them to open in the same instance.