When running a built installer one of the first 'progress' messages displayed at the bottom of the screen during the actual install is "Extracting duplicates...". Anyone know what this refers to ? [ its not text in the project file ]
If my memory's correct, one of the new features of IA 2010 is exactly this: in order to reduce installer size, duplicates files are detected and stored only once. So it seems that in your case you might have duplicated files (that you need to install in different folders for instance) but before proceeding the installer needs to extract those (it must be some special case of storing them).
You can try some manual parsing of the .iap_xml file as all files should be references (however I'm not sure if the feature is really intelligent and also checks speedfolders for instance). In this case I'm afraid that there isn't much you can do, as the check must be done at build time, so it'll be hard to find the duplicates, as the SpeedFolder content is determined at build time...
