Thanks for the suggestion Starship Builder, but I had the same issues with Pepakura2.
Altogether I had three problems:
1. With one version of the file I had an extra 400 or so faces generated between two seperate parts after some boolean hole cutting in Blender. I recut the holes and most of this went away apart from....
2. The boolean opeartion to cut the holes resulted in some very long thin faces and some loose 'flaps' which were only visible at extreme zoom. These had to be manually removed/ refaced.
3. two parts would not transfer to Pepakura. Even if I added new clean parts, they would not transfer. I eventually got around it by deleting the parts, then copying and modifying two similar existing parts.
However, what I can do is export the mesh from blender to an stl file; import it back to blender (seperate and re-texture it) and then re-export as 3ds to pepakura. Then the file is OK and I can add whatever I want. So, it could be something to do with the existing texture mapping (I know pepakura takes stl files too, but you lose the texture mapping).
Anyway I am almost ready for a proper pepakura layout.