My guess is that if you opened each project and clicked Modify > Rescale Project you will find each project has a different resolution.
The thing is, if you are copying slides from one project to another, it behooves you to ensure that both projects are sharing the same project resolution. Otherwise, you will encounter exactly what you are seeing.
Your only options at this point are to either rescale one project so it is the same dimensions as the other, or manipulate the content after you copy and paste the slide(s).
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