To add to this, I've since discovered that if I re-install my MSI, but point it to a different Application folder (eg. c:\program files\some_other_location\ instead of c:\program files\default_location\), then Uninstall it, then the files from the MSM get correctly removed from the new folder and that folder disappears.
In other words, the problem seems somehow specific to the application being installed in the location where I originally installed it. I'm now wondering if there could be something in the Windows Installer System which is referencing the files in the original place and is preventing them from being removed. I'm not entirely sure what to look for, though.
The list of installed products returned by the the
Windows Installer Cleanup Utility doesn't show anything obvious. In fact, if I've uninstalled the application and it's left files behind, there's nothing in the list to indicate that the application is still installed. It doesn't look as if that utility is designed to display anything about installed merge modules, however.
This may be localised to my development system, but it's still a bit frustrating not knowing what's causing it.
Mike.