I came across an issue today whilst sequencing an application on Windows 7 x64 that contained a start menu shortcut to a .MSC file. During sequencing the application launched fine but it would not do so on the client.
The solution is to modify the OSD to point to MMC.exe with the -32 switch and the path to your .MSC file wrapped in quotes:
<CODEBASE HREF="*" GUID="*" PARAMETERS="-32 "%SFT_MNT%\ROOTFOLDER\PathToFile.msc"" FILENAME="%CSIDL_SYSTEM%\mmc.exe" SYSGUARDFILE="*" SIZE="*"/>
You will also need to set the __COMPAT_LAYER environment variable if MMC.exe requests elevation:
This should allow it to work on both x86 and x64 clients.