Software Deployment

I've created a capture of a non msi application using IS. During the generation of the msi I get an entry in the log that "A non-advertised shortcut must be created for "shortcut name." Autorepair cannot be enabled for this shortcut. I can go in and make the corrections afterward to the shortcut to make it advertised using Orca but I was wondering why IS is having this issue. Also if anyone knows how to force IS to set the ALLUSERS=1 instead of the default 2 during the MSI creation process...