Thanks for inquiring Aspose.Slides.
I have observed the requirements shared by you and like to share that you need to set the target pretension slide size to that of source presentation. The default, slide size is 720 x 540. This is the reason why the cloned slides are not properly copied. Please try using the attached sample code on your end and share with us if there is any issue incurring.
String path= @“D:\Aspose Data”;
Presentation peSource = new Presentation(path+“TestFlash1.pptx”);
Presentation peTarget = new Presentation();
peTarget.SlideSize.Size = peSource.SlideSize.Size;
foreach (ISlide slide in peSource.Slides)