This was added "by design" in 2013. I hate it but MSFT think it makes things easier!
You can fix it by adding a registry key:
Open regedit
Navigate to:
HKCU\Software\Microsoft\Office\15.0\PowerPoint\Opt ions]
Add a new DWord and name it RestoreTopology
Set the value to 1
If you are not confident to do this download the key and unzip and double click to add it. Our key is of course tested but it is still at your own risk
http://www.pptalchemy.co.uk/Downloads/dupe.zip