Hi Craig,
There could certainly be an issue, it sounds like. But, I just tested the scenario you described with AdminStudio 10:
--Converting an MSI project using InstallShield
--Converting the same MSI project via automated repackaging in AAC
--Converting the MSI via direct MSI conversion
And each of these generated an OSD file without shortcut information, but containing the appropriate file association information.
The sample project did nothing more than register a copy of notepad.exe with the *.npd file extension (which I picked out of thin air).
What version have you seen this issue in?
Regards,
Cary