What is happening is that the machine you're installing on has an older
version of the Windows Installer than the one that ISX has. The Setup.exe
doesn't bundle the Windows Installer, though you can have a Setup.exe that
will install the Windows Installer if it's not present (see the build
settings in ISX). The version difference doesn't cause any problems and
until an update for the Windows Installer is available simply set Suppress
Launcher Warning to 1 in your build settings in ISX.
Cheers
Craig