It seems that when working with PDFs with version 2, saving the changed PDF creates a corrupt PDF file.
I have created a demo where I apply some stamping and saving twice and after the first save operation the PDF is corrupt (when the PDF version is 2 - when it is an older version all goes well).
I have the project and the file attached.
Just drag and drop the PDF file on the application window while debugging.
You will see the exception thrown.
No errors occur when using older PDF versions.