If they are PPT files (ie the 2003 format) Then you are going to have major problems as the format of the ppt master is completely different to the master in later versions. It is creating extra masters because it doesn't have custom layouts.
You would probably need to create suitable layouts in 2013 and apply them then delete the old masters. Even so you will find the color scheme is also completely different.
In short it's less painful to attack your body with a blunt instrument!
Might help to post an example file.
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