I am having the same issue but all I am doing is merging slides.
using code from http://msdn.microsoft.com/en-us/library/ee361883(v=office.12).aspx
I am trying to merge these 2 files. https://skydrive.live.com/?cid=ee0e0c195f132fb7&id=EE0E0C195F132FB7%21159
there is nothing in the template file and only a blank slide on the presentation file and I still get this message when the files are opened.
To date, no one has put together the definitive example code on merging PowerPoint slides, in a similar way to how DocumentBuilder deals with word-processing documents. It is on the TODO list of projects, but currently there are a few high-priority projects are ahead of this.
When dealing with these types of issues, first of all, make sure that you are taking advantage of the validation features of the Open XML SDK, and that you are generating valid markup.
Another key tool that I use is to basically do a 'binary search' for the code that is generating the markup that is invalid. For example, I cut my program down until it is generating something that validates, and then gradually add in code until I have added code that generates an invalid presentation (or word-processing doc, or spreadsheet). I know it is cumbersome, but sometimes there is no other option. By their very nature, document formats are complicated. This is true for Open XML, PDF, XPS, Rich Text, ODF, HTML/CSS, or any of the other varieties of document formats.