Hi,
I found a workaround that could work for you.You can write a post.bat file to copy the shortcut created for your program item to wherever you want.The only thing you have to do is to create the windows start menu item for your operator interface and include a post.bat file in your installer directory to copy the *.lnk file to the desired location.
The Post.bat file is executed immediatly after the installer finishes.
I am attaching a simple installer that installs the CVI simple operator interface and creates a shortcut for it in the Windows Start menu and on the Desktop.
I am only copying the file from the start menu to the desktop in the post file.
I hope it helps.
Installer.zip:
http://forums.ni.com/attachments/ni/330/7767/1/Installer.zip