The problem appeared in the system with an Office 2013 installed.
Thank you for sharing the details.
As I understand, you are facing the issue after converting from PPT to PPTX and then once you use that PPTX to JPEG, the smart art is missing. I tested with the latest version of Aspose.Slides for .NET v14.6.0 and I am unable to reproduce the issue. Please try with the latest version and let us know if it works fine at your end.
Thanks & Regards,