We were testing one of installers under Vista and the dreaded "User Account Control" dialog was being launched for every shortcut that was created by the installer. Running the applications referenced by the shortcuts did not through the UAC, just the shortcuts.
I took a look the shortcuts and they didn't have a direct link to the apps. Instead they looked like this:
"C:\Program Files\Company\App\UNWISE.EXE" /W1 "C:\Program Files\Company\App\INSTALL.LOG"
This was Wise 9's attempt to mimic the self-repair feature of Microsoft's Windows Installer. If you are using Wise 9 Professional, you can fix this by opening the shortcut action in the setup editor and clearing the self-repair checkbox. If you have the Standard version, you'll have to edit the installer script (.wse) with a text editor. For each shortcut, you would remove the line of script reading 'Flags=01000000' from the Create Shortcut script action code block. This is documented in the Altiris Knowledgebase as article 23832. I found that article by searching the Altiris support forums and I came across this message thread.